From d78c8fdc14081cf20dd07acbc322bc1bde26c199 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Tue, 12 Nov 2024 16:40:45 +0100
Subject: [PATCH 01/16] pass json args to the ssh hpc calls

---
 Makefile                                      |  2 +-
 .../batch_submit_workflow_job.sh              | 55 ++++++++++++-------
 .../wrapper_submit_workflow_job.sh            | 28 ++++++++--
 src/utils/operandi_utils/hpc/constants.py     |  7 ++-
 src/utils/operandi_utils/hpc/nhr_executor.py  | 48 ++++++++--------
 .../{_test_3_hpc => test_3_hpc}/__init__.py   |  0
 .../_test_1_nhr_executor.py}                  |  0
 .../_test_2_nhr_transfer.py}                  |  0
 .../test_3_nhr_combined.py                    |  4 +-
 9 files changed, 91 insertions(+), 53 deletions(-)
 rename tests/tests_utils/{_test_3_hpc => test_3_hpc}/__init__.py (100%)
 rename tests/tests_utils/{_test_3_hpc/test_1_nhr_executor.py => test_3_hpc/_test_1_nhr_executor.py} (100%)
 rename tests/tests_utils/{_test_3_hpc/test_2_nhr_transfer.py => test_3_hpc/_test_2_nhr_transfer.py} (100%)
 rename tests/tests_utils/{_test_3_hpc => test_3_hpc}/test_3_nhr_combined.py (97%)

diff --git a/Makefile b/Makefile
index 778a29b0..026c8c6d 100755
--- a/Makefile
+++ b/Makefile
@@ -119,7 +119,7 @@ run-tests-utils:
 
 run-tests-broker:
 	export $(shell sed 's/=.*//' ./tests/.env)
-	pytest tests/tests_broker/test_*.py -v
+	pytest tests/tests_broker/test_*.py -s -v
 
 run-tests-harvester:
 	export $(shell sed 's/=.*//' ./tests/.env)
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
index 04ebe84c..d5476663 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
@@ -2,6 +2,9 @@
 
 set -e
 
+module purge
+module load jq
+
 # Parameters are as follows:
 # S0 - This batch script
 # S1 - The scratch base for slurm workspaces
@@ -24,18 +27,32 @@ OCRD_MODELS_DIR_IN_NODE="${TMP_LOCAL}/ocrd_models"
 OCRD_MODELS_DIR_IN_DOCKER="/usr/local/share/ocrd-resources"
 BIND_OCRD_MODELS="${OCRD_MODELS_DIR_IN_NODE}/ocrd-resources:${OCRD_MODELS_DIR_IN_DOCKER}"
 
-SCRATCH_BASE=$1
-WORKFLOW_JOB_ID=$2
-NEXTFLOW_SCRIPT_ID=$3
-IN_FILE_GRP=$4
-WORKSPACE_ID=$5
-METS_BASENAME=$6
-CPUS=$7
-RAM=$8
-FORKS=$9
-PAGES=${10}
-USE_METS_SERVER=${11}
-FILE_GROUPS_TO_REMOVE=${12}
+json_args="$1"
+SCRATCH_BASE=$(echo "$json_args" | jq .scratch_base_dir | tr -d '"')
+WORKFLOW_JOB_ID=$(echo "$json_args" | jq .workflow_job_id | tr -d '"')
+NEXTFLOW_SCRIPT_ID=$(echo "$json_args" | jq .nextflow_script_id | tr -d '"')
+IN_FILE_GRP=$(echo "$json_args" | jq .input_file_group | tr -d '"')
+WORKSPACE_ID=$(echo "$json_args" | jq .workspace_id | tr -d '"')
+METS_BASENAME=$(echo "$json_args" | jq .mets_basename | tr -d '"')
+CPUS=$(echo "$json_args" | jq .cpus | tr -d '"')
+RAM=$(echo "$json_args" | jq .ram | tr -d '"')
+FORKS=$(echo "$json_args" | jq .nf_process_forks | tr -d '"')
+PAGES=$(echo "$json_args" | jq .ws_pages_amount | tr -d '"')
+USE_METS_SERVER=$(echo "$json_args" | jq .use_mets_server_bash_flag | tr -d '"')
+FILE_GROUPS_TO_REMOVE=$(echo "$json_args" | jq .file_groups_to_remove | tr -d '"')
+
+echo "SCRATCH_BASE: $SCRATCH_BASE"
+echo "WORKFLOW_JOB_ID: $WORKFLOW_JOB_ID"
+echo "NEXTFLOW_SCRIPT_ID: $NEXTFLOW_SCRIPT_ID"
+echo "IN_FILE_GRP: $IN_FILE_GRP"
+echo "WORKSPACE_ID: $WORKSPACE_ID"
+echo "METS_BASENAME: $METS_BASENAME"
+echo "CPUS: $CPUS"
+echo "RAM: $RAM"
+echo "FORKS: $FORKS"
+echo "PAGES: $PAGES"
+echo "USE_METS_SERVER: $USE_METS_SERVER"
+echo "FILE_GROUPS_TO_REMOVE: $FILE_GROUPS_TO_REMOVE"
 
 WORKFLOW_JOB_DIR="${SCRATCH_BASE}/${WORKFLOW_JOB_ID}"
 NF_SCRIPT_PATH="${WORKFLOW_JOB_DIR}/${NEXTFLOW_SCRIPT_ID}"
@@ -46,13 +63,6 @@ BIND_METS_FILE_PATH="${WORKSPACE_DIR_IN_DOCKER}/${METS_BASENAME}"
 METS_SOCKET_BASENAME="mets_server.sock"
 BIND_METS_SOCKET_PATH="${WORKSPACE_DIR_IN_DOCKER}/${METS_SOCKET_BASENAME}"
 
-hostname
-/opt/slurm/etc/scripts/misc/slurm_resources
-
-module purge
-module load apptainer
-module load nextflow
-# module load spack-user; eval "$(spack load --sh curl%gcc@10.2.0)"
 
 echo "ocrd all SIF path: $SIF_PATH"
 echo "ocrd all SIF path node local: $SIF_PATH_IN_NODE"
@@ -62,6 +72,13 @@ echo "Use mets server: $USE_METS_SERVER"
 echo "Used file group: $IN_FILE_GRP"
 echo "Pages: $PAGES"
 
+module load apptainer
+module load nextflow
+# module load spack-user; eval "$(spack load --sh curl%gcc@10.2.0)"
+
+hostname
+# /opt/slurm/etc/scripts/misc/slurm_resource
+
 # To submit separate jobs for each process in the NF script
 # export NXF_EXECUTOR=slurm
 
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
index a3f6255a..32a02ff5 100644
--- a/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
@@ -22,12 +22,30 @@
 # $18 - Boolean flag showing whether a mets server is utilized or not
 # $19 - File groups to be removed from the workspace after the processing
 
-if [ "$6" == "48h" ] ; then
+module purge
+module load jq
+
+sbatch_args="$1"
+partition=$(echo "$sbatch_args" | jq .partition | tr -d '"')
+deadline_time=$(echo "$sbatch_args" | jq .job_deadline_time | tr -d '"')
+output=$(echo "$sbatch_args" | jq .output_log | tr -d '"')
+cpus_per_task=$(echo "$sbatch_args" | jq .cpus | tr -d '"')
+memory=$(echo "$sbatch_args" | jq .ram | tr -d '"')
+qos=$(echo "$sbatch_args" | jq .qos | tr -d '"')
+batch_script_path=$(echo "$sbatch_args" | jq .batch_script_path | tr -d '"')
+
+if [ "$qos" == "48h" ] ; then
   # QOS not set, the default of 48h is used
-  sbatch --partition="$1" --time="$2" --output="$3" --cpus-per-task="$4" --mem="$5" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}"
+  sbatch --partition="$partition" --time="$deadline_time" --output="$output" --cpus-per-task="$cpus_per_task" --mem="$memory" "$batch_script_path" "$2"
 else
-  sbatch --partition="$1" --time="$2" --output="$3" --cpus-per-task="$4" --mem="$5" --qos="$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}"
+  sbatch --partition="$partition" --time="$deadline_time" --output="$output" --cpus-per-task="$cpus_per_task" --mem="$memory" --qos="$qos" "$batch_script_path" "$2"
 fi
 
-echo "0:$0 1:$1 2:$2 3:$3 4:$4 5:$5 6:$6 7:$7 8:$8 9:$9 10:${10}"
-echo "11:${11} 12:${12} 13:${13} 14:${14} 15:${15} 16:${16} 17:${17} 18:${18} 19:${19}"
+echo "executed wrapper script: $0"
+echo "partition: $partition"
+echo "deadline_time: $deadline_time"
+echo "output: $output"
+echo "cpus_per_task: $cpus_per_task"
+echo "memory: $memory"
+echo "qos: $qos"
+echo "batch_script_path: $batch_script_path"
diff --git a/src/utils/operandi_utils/hpc/constants.py b/src/utils/operandi_utils/hpc/constants.py
index 5e0210d4..1d7ef807 100644
--- a/src/utils/operandi_utils/hpc/constants.py
+++ b/src/utils/operandi_utils/hpc/constants.py
@@ -61,12 +61,13 @@
 HPC_DIR_BATCH_SCRIPTS = "batch_scripts"
 HPC_DIR_SLURM_WORKSPACES = "slurm_workspaces"
 # TODO: Fix the constant file name - it should be automatically resolved
-HPC_BATCH_SUBMIT_WORKFLOW_JOB = f"{HPC_NHR_SCRATCH_EMMY_HDD}/{HPC_DIR_BATCH_SCRIPTS}/batch_submit_workflow_job.sh"
-HPC_WRAPPER_SUBMIT_WORKFLOW_JOB = f"{HPC_NHR_SCRATCH_EMMY_HDD}/{HPC_DIR_BATCH_SCRIPTS}/wrapper_submit_workflow_job.sh"
+# TODO: Fix the naming when releasing the next Operandi version
+HPC_BATCH_SUBMIT_WORKFLOW_JOB = f"{HPC_NHR_SCRATCH_EMMY_HDD}/{HPC_DIR_BATCH_SCRIPTS}/batch_submit_workflow_job2.sh"
+HPC_WRAPPER_SUBMIT_WORKFLOW_JOB = f"{HPC_NHR_SCRATCH_EMMY_HDD}/{HPC_DIR_BATCH_SCRIPTS}/wrapper_submit_workflow_job2.sh"
 HPC_WRAPPER_CHECK_WORKFLOW_JOB_STATUS = f"{HPC_NHR_SCRATCH_EMMY_HDD}/{HPC_DIR_BATCH_SCRIPTS}/wrapper_check_workflow_job_status.sh"
 
 HPC_JOB_DEADLINE_TIME_REGULAR = "48:00:00"
-HPC_JOB_DEADLINE_TIME_TEST = "0:30:00"
+HPC_JOB_DEADLINE_TIME_TEST = "00:30:00"
 HPC_NHR_JOB_DEFAULT_PARTITION = "standard96s:shared"
 HPC_NHR_JOB_TEST_PARTITION = "standard96s:shared"
 
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index 7636f2f2..3f679169 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -1,3 +1,4 @@
+from json import dumps
 from logging import getLogger
 from pathlib import Path
 from time import sleep
@@ -48,30 +49,31 @@ def trigger_slurm_job(
         use_mets_server_bash_flag = "true" if use_mets_server else "false"
 
         command = f"{HPC_WRAPPER_SUBMIT_WORKFLOW_JOB}"
+        sbatch_args = {
+            "partition": partition,
+            "job_deadline_time": job_deadline_time,
+            "output_log": f"{self.slurm_workspaces_dir}/{workflow_job_id}/slurm-job-%J.txt",
+            "cpus": cpus,
+            "ram": f"{ram}G",
+            "qos": qos,
+            "batch_script_path": HPC_BATCH_SUBMIT_WORKFLOW_JOB
+        }
+        regular_args = {
+            "scratch_base_dir": self.slurm_workspaces_dir,
+            "workflow_job_id": workflow_job_id,
+            "nextflow_script_id": nextflow_script_id,
+            "input_file_group": input_file_grp,
+            "workspace_id": workspace_id,
+            "mets_basename": mets_basename,
+            "cpus": cpus,
+            "ram": ram,
+            "nf_process_forks": nf_process_forks,
+            "ws_pages_amount": ws_pages_amount,
+            "use_mets_server_bash_flag": use_mets_server_bash_flag,
+            "file_groups_to_remove": file_groups_to_remove
+        }
 
-        # SBATCH arguments passed to the batch script
-        command += f" {partition}"
-        command += f" {job_deadline_time}"
-        command += f" {self.slurm_workspaces_dir}/{workflow_job_id}/slurm-job-%J.txt"
-        command += f" {cpus}"
-        command += f" {ram}G"
-        command += f" {qos}"
-
-        # Regular arguments passed to the batch script
-        command += f" {HPC_BATCH_SUBMIT_WORKFLOW_JOB}"
-        command += f" {self.slurm_workspaces_dir}"
-        command += f" {workflow_job_id}"
-        command += f" {nextflow_script_id}"
-        command += f" {input_file_grp}"
-        command += f" {workspace_id}"
-        command += f" {mets_basename}"
-        command += f" {cpus}"
-        command += f" {ram}"
-        command += f" {nf_process_forks}"
-        command += f" {ws_pages_amount}"
-        command += f" {use_mets_server_bash_flag}"
-        command += f" {file_groups_to_remove}"
-
+        command += f" '{dumps(sbatch_args)}' '{dumps(regular_args)}'"
         self.logger.info(f"About to execute a force command: {command}")
         output, err, return_code = self.execute_blocking(command)
         self.logger.info(f"Command output: {output}")
diff --git a/tests/tests_utils/_test_3_hpc/__init__.py b/tests/tests_utils/test_3_hpc/__init__.py
similarity index 100%
rename from tests/tests_utils/_test_3_hpc/__init__.py
rename to tests/tests_utils/test_3_hpc/__init__.py
diff --git a/tests/tests_utils/_test_3_hpc/test_1_nhr_executor.py b/tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py
similarity index 100%
rename from tests/tests_utils/_test_3_hpc/test_1_nhr_executor.py
rename to tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py
diff --git a/tests/tests_utils/_test_3_hpc/test_2_nhr_transfer.py b/tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py
similarity index 100%
rename from tests/tests_utils/_test_3_hpc/test_2_nhr_transfer.py
rename to tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py
diff --git a/tests/tests_utils/_test_3_hpc/test_3_nhr_combined.py b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
similarity index 97%
rename from tests/tests_utils/_test_3_hpc/test_3_nhr_combined.py
rename to tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
index 3309b538..73d7ad09 100644
--- a/tests/tests_utils/_test_3_hpc/test_3_nhr_combined.py
+++ b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
@@ -62,7 +62,7 @@ def test_hpc_connector_run_batch_script(
         workflow_job_id=ID_WORKFLOW_JOB, nextflow_script_path=Path(template_workflow),
         input_file_grp=DEFAULT_FILE_GRP, workspace_id=ID_WORKSPACE,
         mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8, use_mets_server=False,
-        file_groups_to_remove="", cpus=2, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
+        file_groups_to_remove="", cpus=2, ram=8, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
         partition=HPC_NHR_JOB_TEST_PARTITION, qos=HPC_JOB_QOS_SHORT)
     finished_successfully = hpc_nhr_command_executor.poll_till_end_slurm_job_state(
         slurm_job_id=slurm_job_id, interval=5, timeout=300)
@@ -84,7 +84,7 @@ def test_hpc_connector_run_batch_script_with_ms(
         workflow_job_id=ID_WORKFLOW_JOB_WITH_MS, nextflow_script_path=Path(template_workflow_with_ms),
         input_file_grp=DEFAULT_FILE_GRP, workspace_id=ID_WORKSPACE_WITH_MS,
         mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8,
-        use_mets_server=True, file_groups_to_remove="", cpus=3, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
+        use_mets_server=True, file_groups_to_remove="", cpus=3, ram=8, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
         partition=HPC_NHR_JOB_TEST_PARTITION, qos=HPC_JOB_QOS_SHORT)
     finished_successfully = hpc_nhr_command_executor.poll_till_end_slurm_job_state(
         slurm_job_id=slurm_job_id, interval=5, timeout=300)

From 17c15f66d616f69cc2817a684c278d3e4a0fbf77 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Tue, 12 Nov 2024 17:02:02 +0100
Subject: [PATCH 02/16] clean: remove redundant comments

---
 .../batch_submit_workflow_job.sh              | 70 ++++---------------
 .../wrapper_submit_workflow_job.sh            | 32 +--------
 src/utils/operandi_utils/hpc/nhr_executor.py  |  2 +-
 ...nhr_executor.py => test_1_nhr_executor.py} |  0
 ...nhr_transfer.py => test_2_nhr_transfer.py} |  0
 .../test_3_hpc/test_3_nhr_combined.py         |  4 +-
 6 files changed, 17 insertions(+), 91 deletions(-)
 rename tests/tests_utils/test_3_hpc/{_test_1_nhr_executor.py => test_1_nhr_executor.py} (100%)
 rename tests/tests_utils/test_3_hpc/{_test_2_nhr_transfer.py => test_2_nhr_transfer.py} (100%)

diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
index d5476663..849b6ae3 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
@@ -4,28 +4,15 @@ set -e
 
 module purge
 module load jq
+module load apptainer
+module load nextflow
+# module load spack-user; eval "$(spack load --sh curl%gcc@10.2.0)"
 
-# Parameters are as follows:
-# S0 - This batch script
-# S1 - The scratch base for slurm workspaces
-# $2 - Workflow job id
-# $3 - Nextflow script id
-# $4 - Entry input file group
-# $5 - Workspace id
-# $6 - Mets basename - default "mets.xml"
-# $7 - CPUs for the Nextflow processes
-# $8 - RAM for the Nextflow processes
-# $9 - Amount of forks per OCR-D processor in the NF script
-# $10 - Amount of pages in the workspace
-# $11 - Boolean flag showing whether a mets server is utilized or not
-# $12 - File groups to be removed from the workspace after the processing
+hostname
+# /opt/slurm/etc/scripts/misc/slurm_resource
 
-SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_all_maximum_image.sif"
-SIF_PATH_IN_NODE="${TMP_LOCAL}/ocrd_all_maximum_image.sif"
-OCRD_MODELS_DIR="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_models"
-OCRD_MODELS_DIR_IN_NODE="${TMP_LOCAL}/ocrd_models"
-OCRD_MODELS_DIR_IN_DOCKER="/usr/local/share/ocrd-resources"
-BIND_OCRD_MODELS="${OCRD_MODELS_DIR_IN_NODE}/ocrd-resources:${OCRD_MODELS_DIR_IN_DOCKER}"
+# To submit separate jobs for each process in the NF script
+# export NXF_EXECUTOR=slurm
 
 json_args="$1"
 SCRATCH_BASE=$(echo "$json_args" | jq .scratch_base_dir | tr -d '"')
@@ -41,18 +28,12 @@ PAGES=$(echo "$json_args" | jq .ws_pages_amount | tr -d '"')
 USE_METS_SERVER=$(echo "$json_args" | jq .use_mets_server_bash_flag | tr -d '"')
 FILE_GROUPS_TO_REMOVE=$(echo "$json_args" | jq .file_groups_to_remove | tr -d '"')
 
-echo "SCRATCH_BASE: $SCRATCH_BASE"
-echo "WORKFLOW_JOB_ID: $WORKFLOW_JOB_ID"
-echo "NEXTFLOW_SCRIPT_ID: $NEXTFLOW_SCRIPT_ID"
-echo "IN_FILE_GRP: $IN_FILE_GRP"
-echo "WORKSPACE_ID: $WORKSPACE_ID"
-echo "METS_BASENAME: $METS_BASENAME"
-echo "CPUS: $CPUS"
-echo "RAM: $RAM"
-echo "FORKS: $FORKS"
-echo "PAGES: $PAGES"
-echo "USE_METS_SERVER: $USE_METS_SERVER"
-echo "FILE_GROUPS_TO_REMOVE: $FILE_GROUPS_TO_REMOVE"
+SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_all_maximum_image.sif"
+SIF_PATH_IN_NODE="${TMP_LOCAL}/ocrd_all_maximum_image.sif"
+OCRD_MODELS_DIR="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_models"
+OCRD_MODELS_DIR_IN_NODE="${TMP_LOCAL}/ocrd_models"
+OCRD_MODELS_DIR_IN_DOCKER="/usr/local/share/ocrd-resources"
+BIND_OCRD_MODELS="${OCRD_MODELS_DIR_IN_NODE}/ocrd-resources:${OCRD_MODELS_DIR_IN_DOCKER}"
 
 WORKFLOW_JOB_DIR="${SCRATCH_BASE}/${WORKFLOW_JOB_ID}"
 NF_SCRIPT_PATH="${WORKFLOW_JOB_DIR}/${NEXTFLOW_SCRIPT_ID}"
@@ -63,7 +44,6 @@ BIND_METS_FILE_PATH="${WORKSPACE_DIR_IN_DOCKER}/${METS_BASENAME}"
 METS_SOCKET_BASENAME="mets_server.sock"
 BIND_METS_SOCKET_PATH="${WORKSPACE_DIR_IN_DOCKER}/${METS_SOCKET_BASENAME}"
 
-
 echo "ocrd all SIF path: $SIF_PATH"
 echo "ocrd all SIF path node local: $SIF_PATH_IN_NODE"
 echo "Workspace dir: $WORKSPACE_DIR"
@@ -72,17 +52,6 @@ echo "Use mets server: $USE_METS_SERVER"
 echo "Used file group: $IN_FILE_GRP"
 echo "Pages: $PAGES"
 
-module load apptainer
-module load nextflow
-# module load spack-user; eval "$(spack load --sh curl%gcc@10.2.0)"
-
-hostname
-# /opt/slurm/etc/scripts/misc/slurm_resource
-
-# To submit separate jobs for each process in the NF script
-# export NXF_EXECUTOR=slurm
-
-
 # Define functions to be used
 check_existence_of_paths() {
   # The SIF file of the OCR-D All docker image must be previously created
@@ -159,13 +128,6 @@ unzip_workflow_job_dir() {
 }
 
 start_mets_server() {
-  # TODO: Would be better to start the mets server as an instance, but this is still broken
-  # apptainer instance start \
-  #   --bind "${BIND_WORKSPACE_DIR}" \
-  #   "${SIF_PATH_IN_NODE}" \
-  #   instance_mets_server \
-  #  ocrd workspace -U "${BIND_METS_SOCKET_PATH}" -d "${WORKSPACE_DIR_IN_DOCKER}" server start
-
   if [ "$1" == "true" ] ; then
     echo "Starting the mets server for the specific workspace in the background"
     apptainer exec \
@@ -178,12 +140,6 @@ start_mets_server() {
 }
 
 stop_mets_server() {
-  # Not supported in the HPC (the version there is <7.40)
-  # curl -X DELETE --unix-socket "${WORKSPACE_DIR}/${METS_SOCKET_BASENAME}" "http://localhost/"
-
-  # TODO Stop the instance here
-  # singularity instance stop instance_mets_server
-
   if [ "$1" == "true" ] ; then
     echo "Stopping the mets server"
     apptainer exec \
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
index 32a02ff5..b662459b 100644
--- a/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
@@ -1,27 +1,5 @@
 #!/bin/bash
 
-# $0 - This bash script
-# $1 - Slurm parameter - partition
-# $2 - Slurm parameter - time
-# $3 - Slurm parameter - output
-# $4 - Slurm parameter - cpus-per-task
-# $5 - Slurm parameter - mem
-# $6 - Slurm parameter - qos
-
-# $7 - The batch script path to execute
-# $8 - The scratch base for slurm workspaces
-# $9 - Workflow job id
-# $10 - Nextflow script id
-# $11 - Entry input file group
-# $12 - Workspace id
-# $13 - Mets basename - default "mets.xml"
-# $14 - CPUs for the Nextflow processes
-# $15 - RAM for the Nextflow processes
-# $16 - Amount of forks per OCR-D processor in the NF script
-# $17 - Amount of pages in the workspace
-# $18 - Boolean flag showing whether a mets server is utilized or not
-# $19 - File groups to be removed from the workspace after the processing
-
 module purge
 module load jq
 
@@ -34,18 +12,10 @@ memory=$(echo "$sbatch_args" | jq .ram | tr -d '"')
 qos=$(echo "$sbatch_args" | jq .qos | tr -d '"')
 batch_script_path=$(echo "$sbatch_args" | jq .batch_script_path | tr -d '"')
 
+# $2 is a json of regular arguments used inside the `batch_submit_workflow_job.sh`
 if [ "$qos" == "48h" ] ; then
   # QOS not set, the default of 48h is used
   sbatch --partition="$partition" --time="$deadline_time" --output="$output" --cpus-per-task="$cpus_per_task" --mem="$memory" "$batch_script_path" "$2"
 else
   sbatch --partition="$partition" --time="$deadline_time" --output="$output" --cpus-per-task="$cpus_per_task" --mem="$memory" --qos="$qos" "$batch_script_path" "$2"
 fi
-
-echo "executed wrapper script: $0"
-echo "partition: $partition"
-echo "deadline_time: $deadline_time"
-echo "output: $output"
-echo "cpus_per_task: $cpus_per_task"
-echo "memory: $memory"
-echo "qos: $qos"
-echo "batch_script_path: $batch_script_path"
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index 3f679169..d450cbc6 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -72,8 +72,8 @@ def trigger_slurm_job(
             "use_mets_server_bash_flag": use_mets_server_bash_flag,
             "file_groups_to_remove": file_groups_to_remove
         }
-
         command += f" '{dumps(sbatch_args)}' '{dumps(regular_args)}'"
+
         self.logger.info(f"About to execute a force command: {command}")
         output, err, return_code = self.execute_blocking(command)
         self.logger.info(f"Command output: {output}")
diff --git a/tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py b/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
similarity index 100%
rename from tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py
rename to tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
diff --git a/tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py b/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
similarity index 100%
rename from tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py
rename to tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
diff --git a/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
index 73d7ad09..3309b538 100644
--- a/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
+++ b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
@@ -62,7 +62,7 @@ def test_hpc_connector_run_batch_script(
         workflow_job_id=ID_WORKFLOW_JOB, nextflow_script_path=Path(template_workflow),
         input_file_grp=DEFAULT_FILE_GRP, workspace_id=ID_WORKSPACE,
         mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8, use_mets_server=False,
-        file_groups_to_remove="", cpus=2, ram=8, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
+        file_groups_to_remove="", cpus=2, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
         partition=HPC_NHR_JOB_TEST_PARTITION, qos=HPC_JOB_QOS_SHORT)
     finished_successfully = hpc_nhr_command_executor.poll_till_end_slurm_job_state(
         slurm_job_id=slurm_job_id, interval=5, timeout=300)
@@ -84,7 +84,7 @@ def test_hpc_connector_run_batch_script_with_ms(
         workflow_job_id=ID_WORKFLOW_JOB_WITH_MS, nextflow_script_path=Path(template_workflow_with_ms),
         input_file_grp=DEFAULT_FILE_GRP, workspace_id=ID_WORKSPACE_WITH_MS,
         mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8,
-        use_mets_server=True, file_groups_to_remove="", cpus=3, ram=8, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
+        use_mets_server=True, file_groups_to_remove="", cpus=3, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
         partition=HPC_NHR_JOB_TEST_PARTITION, qos=HPC_JOB_QOS_SHORT)
     finished_successfully = hpc_nhr_command_executor.poll_till_end_slurm_job_state(
         slurm_job_id=slurm_job_id, interval=5, timeout=300)

From 5caaa98f2f84125132ee62b0bfae8b220af745ee Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Sun, 24 Nov 2024 21:09:04 +0100
Subject: [PATCH 03/16] another portion of changes to slim containers

---
 .../batch_check_ocrd_all_version.sh           |  94 ++++++-
 .../batch_create_ocrd_all_maximum_sif.sh      |   2 +-
 .../batch_download_ocrd_all_models.sh         |   4 +-
 .../batch_submit_workflow_job.sh              | 238 ++++++++++--------
 src/utils/operandi_utils/hpc/constants.py     |   5 +-
 src/utils/operandi_utils/hpc/nhr_connector.py |   7 +-
 src/utils/operandi_utils/hpc/nhr_executor.py  |  86 ++++++-
 ...hr_executor.py => _test_1_nhr_executor.py} |   0
 ...hr_transfer.py => _test_2_nhr_transfer.py} |   0
 9 files changed, 316 insertions(+), 120 deletions(-)
 rename tests/tests_utils/test_3_hpc/{test_1_nhr_executor.py => _test_1_nhr_executor.py} (100%)
 rename tests/tests_utils/test_3_hpc/{test_2_nhr_transfer.py => _test_2_nhr_transfer.py} (100%)

diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh
index 24466582..35372adc 100644
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
-#SBATCH --partition standard96:shared
-#SBATCH --time 00:05:00
+#SBATCH --partition standard96s:shared
+#SBATCH --time 00:20:00
 #SBATCH --qos 2h
 #SBATCH --output check_ocrd_all_version_job-%J.txt
 #SBATCH --cpus-per-task 1
@@ -9,12 +9,96 @@
 set -e
 
 hostname
-/opt/slurm/etc/scripts/misc/slurm_resources
+# /opt/slurm/etc/scripts/misc/slurm_resources
 
 module purge
 module load apptainer
-SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_all_maximum_image.sif"
+SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
 
-apptainer exec "$SIF_PATH" ocrd --version
 apptainer exec "$SIF_PATH" ocrd-tesserocr-recognize --dump-module-dir
 apptainer exec "$SIF_PATH" ls -la /models
+
+ocrd_processors=(
+"ocrd-anybaseocr-binarize"
+"ocrd-anybaseocr-block-segmentation"
+"ocrd-anybaseocr-crop"
+"ocrd-anybaseocr-deskew"
+"ocrd-anybaseocr-dewarp"
+"ocrd-anybaseocr-layout-analysis"
+"ocrd-anybaseocr-textline"
+"ocrd-anybaseocr-tiseg"
+"ocrd-calamari-recognize"
+"ocrd-cis-align"
+"ocrd-cis-data"
+"ocrd-cis-ocropy-binarize"
+"ocrd-cis-ocropy-clip"
+"ocrd-cis-ocropy-denoise"
+"ocrd-cis-ocropy-deskew"
+"ocrd-cis-ocropy-dewarp"
+"ocrd-cis-ocropy-recognize"
+"ocrd-cis-ocropy-resegment"
+"ocrd-cis-ocropy-segment"
+"ocrd-cis-ocropy-train"
+"ocrd-cis-postcorrect"
+"ocrd-cor-asv-ann-align"
+"ocrd-cor-asv-ann-evaluate"
+"ocrd-cor-asv-ann-join"
+"ocrd-cor-asv-ann-mark"
+"ocrd-cor-asv-ann-process"
+"ocrd-detectron2-segment"
+"ocrd-dinglehopper"
+"ocrd-docstruct"
+"ocrd-doxa-binarize"
+"ocrd-dummy"
+"ocrd-eynollah-segment"
+"ocrd-fileformat-transform"
+"ocrd-froc-recognize"
+"ocrd-im6convert"
+"ocrd-import"
+"ocrd-keraslm-rate"
+"ocrd-kraken-binarize"
+"ocrd-kraken-recognize"
+"ocrd-kraken-segment"
+"ocrd-make"
+"ocrd-nmalign-merge"
+"ocrd-olahd-client"
+"ocrd-olena-binarize"
+"ocrd-page2alto-transform"
+"ocrd-pagetopdf"
+"ocrd-page-transform"
+"ocrd-preprocess-image"
+"ocrd-repair-inconsistencies"
+"ocrd-sbb-binarize"
+"ocrd-segment-evaluate"
+"ocrd-segment-extract-glyphs"
+"ocrd-segment-extract-lines"
+"ocrd-segment-extract-pages"
+"ocrd-segment-extract-regions"
+"ocrd-segment-extract-words"
+"ocrd-segment-from-coco"
+"ocrd-segment-from-masks"
+"ocrd-segment-project"
+"ocrd-segment-repair"
+"ocrd-segment-replace-original"
+"ocrd-segment-replace-page"
+"ocrd-segment-replace-text"
+"ocrd-skimage-binarize"
+"ocrd-skimage-denoise"
+"ocrd-skimage-denoise-raw"
+"ocrd-skimage-normalize"
+"ocrd-tesserocr-binarize"
+"ocrd-tesserocr-crop"
+"ocrd-tesserocr-deskew"
+"ocrd-tesserocr-fontshape"
+"ocrd-tesserocr-recognize"
+"ocrd-tesserocr-segment"
+"ocrd-tesserocr-segment-line"
+"ocrd-tesserocr-segment-region"
+"ocrd-tesserocr-segment-table"
+"ocrd-tesserocr-segment-word"
+)
+
+for ocrd_processor in "${ocrd_processors[@]}"
+do
+  echo -n "$ocrd_processor " & apptainer exec "$SIF_PATH" "$ocrd_processor" --version || true
+done
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh
index 96500594..7ac3f522 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-#SBATCH --partition standard96:shared
+#SBATCH --partition standard96s:shared
 #SBATCH --time 2:00:00
 #SBATCH --output create_ocrd_all_sif_job-%J.txt
 #SBATCH --cpus-per-task 16
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
index 05e543ab..fffdf2d5 100644
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-#SBATCH --partition standard96:shared
+#SBATCH --partition standard96s:shared
 #SBATCH --time 6:00:00
 #SBATCH --output download_all_ocrd_models_job-%J.txt
 #SBATCH --cpus-per-task 16
@@ -14,7 +14,7 @@ hostname
 /opt/slurm/etc/scripts/misc/slurm_resources
 
 # This sif file is generated with another batch script
-SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_all_maximum_image.sif"
+SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
 OCRD_MODELS_DIR="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_models"
 OCRD_MODELS_DIR_IN_DOCKER="/usr/local/share"
 
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
index 849b6ae3..8f807194 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
@@ -14,92 +14,129 @@ hostname
 # To submit separate jobs for each process in the NF script
 # export NXF_EXECUTOR=slurm
 
+# TODO: Use the -r (or --raw-output) option to emit raw strings as output:
 json_args="$1"
+
+ocrd_processor_images=()
+mapfile -t ocrd_processor_images < <(echo "$json_args" | jq .ocrd_processor_images | tr -d '"' | tr "," "\n")
+echo "Ocrd total images in request: ${#ocrd_processor_images[@]}"
+echo "Ocrd images: "
+for ocrd_image in "${ocrd_processor_images[@]}"
+do
+   echo -n "${ocrd_image} "
+done
+
+PROJECT_BASE_DIR=$(echo "$json_args" | jq .project_base_dir | tr -d '"')
 SCRATCH_BASE=$(echo "$json_args" | jq .scratch_base_dir | tr -d '"')
 WORKFLOW_JOB_ID=$(echo "$json_args" | jq .workflow_job_id | tr -d '"')
-NEXTFLOW_SCRIPT_ID=$(echo "$json_args" | jq .nextflow_script_id | tr -d '"')
-IN_FILE_GRP=$(echo "$json_args" | jq .input_file_group | tr -d '"')
 WORKSPACE_ID=$(echo "$json_args" | jq .workspace_id | tr -d '"')
-METS_BASENAME=$(echo "$json_args" | jq .mets_basename | tr -d '"')
-CPUS=$(echo "$json_args" | jq .cpus | tr -d '"')
-RAM=$(echo "$json_args" | jq .ram | tr -d '"')
-FORKS=$(echo "$json_args" | jq .nf_process_forks | tr -d '"')
-PAGES=$(echo "$json_args" | jq .ws_pages_amount | tr -d '"')
 USE_METS_SERVER=$(echo "$json_args" | jq .use_mets_server_bash_flag | tr -d '"')
 FILE_GROUPS_TO_REMOVE=$(echo "$json_args" | jq .file_groups_to_remove | tr -d '"')
 
-SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_all_maximum_image.sif"
-SIF_PATH_IN_NODE="${TMP_LOCAL}/ocrd_all_maximum_image.sif"
-OCRD_MODELS_DIR="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_models"
-OCRD_MODELS_DIR_IN_NODE="${TMP_LOCAL}/ocrd_models"
-OCRD_MODELS_DIR_IN_DOCKER="/usr/local/share/ocrd-resources"
-BIND_OCRD_MODELS="${OCRD_MODELS_DIR_IN_NODE}/ocrd-resources:${OCRD_MODELS_DIR_IN_DOCKER}"
-
-WORKFLOW_JOB_DIR="${SCRATCH_BASE}/${WORKFLOW_JOB_ID}"
-NF_SCRIPT_PATH="${WORKFLOW_JOB_DIR}/${NEXTFLOW_SCRIPT_ID}"
-WORKSPACE_DIR="${WORKFLOW_JOB_DIR}/${WORKSPACE_ID}"
-WORKSPACE_DIR_IN_DOCKER="/ws_data"
-BIND_WORKSPACE_DIR="${WORKSPACE_DIR}:${WORKSPACE_DIR_IN_DOCKER}"
-BIND_METS_FILE_PATH="${WORKSPACE_DIR_IN_DOCKER}/${METS_BASENAME}"
-METS_SOCKET_BASENAME="mets_server.sock"
-BIND_METS_SOCKET_PATH="${WORKSPACE_DIR_IN_DOCKER}/${METS_SOCKET_BASENAME}"
-
-echo "ocrd all SIF path: $SIF_PATH"
-echo "ocrd all SIF path node local: $SIF_PATH_IN_NODE"
+WORKFLOW_JOB_DIR=$(echo "$json_args" | jq .hpc_workflow_job_dir | tr -d '"')
+WORKSPACE_DIR=$(echo "$json_args" | jq .hpc_workspace_dir | tr -d '"')
+NF_RUN_COMMAND=$(echo "$json_args" | jq .nf_run_command | tr -d '"')
+START_METS_SERVER_COMMAND=$(echo "$json_args" | jq .start_mets_server_command | tr -d '"')
+STOP_METS_SERVER_COMMAND=$(echo "$json_args" | jq .stop_mets_server_command | tr -d '"')
+LIST_FILE_GROUPS_COMMAND=$(echo "$json_args" | jq .list_file_groups_command | tr -d '"')
+REMOVE_FILE_GROUP_COMMAND=$(echo "$json_args" | jq .remove_file_group_command | tr -d '"')
+
+PROJECT_DIR_OCRD_MODELS="${PROJECT_BASE_DIR}/ocrd_models"
+PROJECT_DIR_PROCESSOR_SIFS="${PROJECT_BASE_DIR}/ocrd_processor_sifs"
+PROJECT_SIF_PATH_OCRD_ALL="${PROJECT_BASE_DIR}/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
+
+NODE_DIR_OCRD_MODELS="${TMP_LOCAL}/ocrd_models"
+NODE_DIR_PROCESSOR_SIFS="${TMP_LOCAL}/ocrd_processor_sifs"
+NODE_SIF_PATH_OCRD_ALL="${TMP_LOCAL}/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
+
+echo ""
+echo "Project dir ocrd models: $PROJECT_DIR_OCRD_MODELS"
+echo "Project dir processor sifs: $PROJECT_DIR_PROCESSOR_SIFS"
+echo "Project sif path ocrd all: $PROJECT_SIF_PATH_OCRD_ALL"
+echo "Node dir ocrd models: $NODE_DIR_OCRD_MODELS"
+echo "Node dir processor sifs: $NODE_DIR_PROCESSOR_SIFS"
+echo "Node sif path ocrd all: $NODE_SIF_PATH_OCRD_ALL"
+echo ""
+
 echo "Workspace dir: $WORKSPACE_DIR"
-echo "Nextflow script path: $NF_SCRIPT_PATH"
 echo "Use mets server: $USE_METS_SERVER"
-echo "Used file group: $IN_FILE_GRP"
-echo "Pages: $PAGES"
 
-# Define functions to be used
-check_existence_of_paths() {
-  # The SIF file of the OCR-D All docker image must be previously created
-  if [ ! -f "${SIF_PATH}" ]; then
-    echo "Required ocrd_all_image sif file not found at: ${SIF_PATH}"
-    exit 1
-  fi
-  echo "Required ocrd_all_image sif file found at: ${SIF_PATH}"
+echo ""
+echo "Nf run command with Node placeholders: $NF_RUN_COMMAND"
+NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
+NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_NODE_DIR_OCRD_MODELS/$NODE_DIR_OCRD_MODELS}"
+NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_CMD_WRAPPER/\'}"
+echo ""
+echo "Nf run command without placeholders: $NF_RUN_COMMAND"
+echo ""
 
-  # Models directory must be previously filled with OCR-D models
-  if [ ! -d "${OCRD_MODELS_DIR}" ]; then
-    echo "Ocrd models directory not found at: ${OCRD_MODELS_DIR}"
-    exit 1
-  fi
-  echo "Ocrd models directory found at: ${OCRD_MODELS_DIR}"
+echo "Replacing ocrd core image sif placeholder of commands"
+START_METS_SERVER_COMMAND="${START_METS_SERVER_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
+STOP_METS_SERVER_COMMAND="${STOP_METS_SERVER_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
+LIST_FILE_GROUPS_COMMAND="${LIST_FILE_GROUPS_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
+REMOVE_FILE_GROUP_COMMAND="${REMOVE_FILE_GROUP_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
+echo ""
 
+check_existence_of_dir_scratch_base(){
   if [ ! -d "${SCRATCH_BASE}" ]; then
+    echo "Creating non-existing SCRATCH_BASE folder"
     mkdir -p "${SCRATCH_BASE}"
   fi
-
   if [ ! -d "${SCRATCH_BASE}" ]; then
-    echo "Required scratch base dir was not created: ${SCRATCH_BASE}"
+    echo "Required scratch base dir was not found: ${SCRATCH_BASE}"
     exit 1
   fi
   echo "Scratch base found/created at: ${SCRATCH_BASE}"
 }
 
-clear_data_from_computing_node() {
-  echo "If existing, removing the SIF from the computing node, path: ${SIF_PATH_IN_NODE}"
-  rm -f "${SIF_PATH_IN_NODE}"
-  echo "If existing, removing the OCR-D models from the computing node, path: ${OCRD_MODELS_DIR_IN_NODE}"
-  rm -rf "${OCRD_MODELS_DIR_IN_NODE}"
+check_existence_of_dir_ocrd_models(){
+  # Models directory must be previously filled with OCR-D models
+  if [ ! -d "${PROJECT_DIR_OCRD_MODELS}" ]; then
+    echo "Ocrd models directory not found at: ${PROJECT_DIR_OCRD_MODELS}"
+    exit 1
+  fi
+  echo "Ocrd models directory found at: ${PROJECT_DIR_OCRD_MODELS}"
 }
 
-transfer_requirements_to_node_storage() {
-  cp "${SIF_PATH}" "${SIF_PATH_IN_NODE}"
-  # Check if transfer successful
-  if [ ! -f "${SIF_PATH_IN_NODE}" ]; then
-    echo "Required ocrd_all_image sif file not found at node local storage: ${SIF_PATH_IN_NODE}"
+check_existence_of_sif_path_ocrd_all(){
+  # The SIF file of the OCR-D All docker image must be previously created
+  if [ ! -f "${PROJECT_SIF_PATH_OCRD_ALL}" ]; then
+    echo "Required ocrd_all_image sif file not found at: ${PROJECT_SIF_PATH_OCRD_ALL}"
     exit 1
-  else
-    echo "Successfully transferred SIF to node local storage"
-    apptainer exec "$SIF_PATH_IN_NODE" ocrd --version
   fi
+  echo "Required ocrd_all_image sif file found at: ${PROJECT_SIF_PATH_OCRD_ALL}"
+}
+
+check_existence_of_ocrd_processor_images_to_be_used(){
+  for ocrd_image in "${ocrd_processor_images[@]}"
+  do
+    image_path="${PROJECT_DIR_PROCESSOR_SIFS}/${ocrd_image}"
+    if [ ! -f "$image_path" ]; then
+      echo "Expected ocrd processor image not found at: $image_path"
+      exit 1
+    fi
+  done
+}
 
-  cp -R "${OCRD_MODELS_DIR}" "${OCRD_MODELS_DIR_IN_NODE}"
-  if [ ! -d "${OCRD_MODELS_DIR_IN_NODE}" ]; then
-    echo "Ocrd models directory not found at node local storage: ${OCRD_MODELS_DIR_IN_NODE}"
+check_existence_of_paths() {
+  check_existence_of_dir_scratch_base
+  check_existence_of_dir_ocrd_models
+  check_existence_of_sif_path_ocrd_all
+  check_existence_of_ocrd_processor_images_to_be_used
+}
+
+clear_data_from_computing_node() {
+  echo ""
+  echo "Removing the OCR-D models directory from the computing node, path: ${NODE_DIR_OCRD_MODELS}"
+  rm -rf "${NODE_DIR_OCRD_MODELS}"
+  echo "Removing the OCR-D processor images (SIF) directory from the computing node, path: ${NODE_DIR_PROCESSOR_SIFS}"
+  rm -rf "${NODE_DIR_PROCESSOR_SIFS}"
+}
+
+transfer_to_node_storage_processor_models(){
+  cp -R "${PROJECT_DIR_OCRD_MODELS}" "${NODE_DIR_OCRD_MODELS}"
+  if [ ! -d "${NODE_DIR_OCRD_MODELS}" ]; then
+    echo "Ocrd models directory not found at node local storage: ${NODE_DIR_OCRD_MODELS}"
     clear_data_from_computing_node
     exit 1
   else
@@ -107,6 +144,38 @@ transfer_requirements_to_node_storage() {
   fi
 }
 
+transfer_to_node_storage_processor_images(){
+  if [ ! -d "${NODE_DIR_PROCESSOR_SIFS}" ]; then
+    echo "Creating non-existing processor sif images dir: $NODE_DIR_PROCESSOR_SIFS"
+    mkdir -p "${NODE_DIR_PROCESSOR_SIFS}"
+  fi
+  if [ ! -d "${NODE_DIR_PROCESSOR_SIFS}" ]; then
+    echo "Required node processor sif images dir was not found: ${NODE_DIR_PROCESSOR_SIFS}"
+    exit 1
+  fi
+
+  for ocrd_image in "${ocrd_processor_images[@]}"
+  do
+    ocrd_image_path="${PROJECT_DIR_PROCESSOR_SIFS}/${ocrd_image}"
+    node_ocrd_image_path="${NODE_DIR_PROCESSOR_SIFS}/${ocrd_image}"
+    if [ ! -f "$ocrd_image_path" ]; then
+      echo "Expected ocrd processor image not found at: $ocrd_image_path"
+      exit 1
+    else
+      echo "Transferring ocrd processor image to the compute node: ${ocrd_image}"
+      cp "${ocrd_image_path}" "${node_ocrd_image_path}"
+      echo "Ocrd processor image was transferred to: ${node_ocrd_image_path}"
+      if [ ! -f "${node_ocrd_image_path}" ]; then
+        echo "Expected ocrd processor image was copied but not found locally at: ${node_ocrd_image_path}"
+        exit 1
+      fi
+    fi
+  done
+  echo ""
+  apptainer exec "$NODE_SIF_PATH_OCRD_ALL" ocrd --version
+  echo ""
+}
+
 unzip_workflow_job_dir() {
   if [ ! -f "${WORKFLOW_JOB_DIR}.zip" ]; then
     echo "Required scratch slurm workspace zip is not available: ${WORKFLOW_JOB_DIR}.zip"
@@ -130,55 +199,25 @@ unzip_workflow_job_dir() {
 start_mets_server() {
   if [ "$1" == "true" ] ; then
     echo "Starting the mets server for the specific workspace in the background"
-    apptainer exec \
-      --bind "${BIND_WORKSPACE_DIR}" \
-      "${SIF_PATH_IN_NODE}" \
-      ocrd workspace -U "${BIND_METS_SOCKET_PATH}" -d "${WORKSPACE_DIR_IN_DOCKER}" server start \
-      > "${WORKSPACE_DIR}/mets_server.log" 2>&1 &
+    eval "$START_METS_SERVER_COMMAND"
+    sleep 10
   fi
-  sleep 10
 }
 
 stop_mets_server() {
   if [ "$1" == "true" ] ; then
     echo "Stopping the mets server"
-    apptainer exec \
-      --bind "${BIND_WORKSPACE_DIR}" \
-      "${SIF_PATH_IN_NODE}" \
-      ocrd workspace -U "${BIND_METS_SOCKET_PATH}" -d "${WORKSPACE_DIR_IN_DOCKER}" server stop
+    eval "$STOP_METS_SERVER_COMMAND"
   fi
 }
 
 execute_nextflow_workflow() {
-  local APPTAINER_CMD="apptainer exec --bind ${BIND_WORKSPACE_DIR} --bind ${BIND_OCRD_MODELS} --env OCRD_METS_CACHING=false ${SIF_PATH_IN_NODE}"
   if [ "$1" == "true" ] ; then
     echo "Executing the nextflow workflow with mets server"
-    nextflow run "${NF_SCRIPT_PATH}" \
-    -ansi-log false \
-    -with-report \
-    --input_file_group "${IN_FILE_GRP}" \
-    --mets "${BIND_METS_FILE_PATH}" \
-    --mets_socket "${BIND_METS_SOCKET_PATH}" \
-    --workspace_dir "${WORKSPACE_DIR_IN_DOCKER}" \
-    --pages "${PAGES}" \
-    --singularity_wrapper "${APPTAINER_CMD}" \
-    --cpus "${CPUS}" \
-    --ram "${RAM}" \
-    --forks "${FORKS}"
   else
     echo "Executing the nextflow workflow without mets server"
-    nextflow run "${NF_SCRIPT_PATH}" \
-    -ansi-log false \
-    -with-report \
-    --input_file_group "${IN_FILE_GRP}" \
-    --mets "${BIND_METS_FILE_PATH}" \
-    --workspace_dir "${WORKSPACE_DIR_IN_DOCKER}" \
-    --pages "${PAGES}" \
-    --singularity_wrapper "${APPTAINER_CMD}" \
-    --cpus "${CPUS}" \
-    --ram "${RAM}" \
-    --forks "${FORKS}"
   fi
+  eval "$NF_RUN_COMMAND"
 
   case $? in
     0) echo "The nextflow workflow execution has finished successfully" ;;
@@ -188,7 +227,7 @@ execute_nextflow_workflow() {
 
 list_file_groups_from_workspace() {
     all_file_groups=()
-    mapfile -t all_file_groups < <(apptainer exec --bind "${BIND_WORKSPACE_DIR}" "${SIF_PATH_IN_NODE}" ocrd workspace -d "${WORKSPACE_DIR_IN_DOCKER}" list-group)
+    mapfile -t all_file_groups < <($LIST_FILE_GROUPS_COMMAND)
     file_groups_length=${#all_file_groups[@]}
     echo -n "File groups: "
     for file_group in "${all_file_groups[@]}"
@@ -201,9 +240,8 @@ list_file_groups_from_workspace() {
 
 remove_file_group_from_workspace() {
   echo "Removing file group: $1"
-  apptainer exec --bind "${BIND_WORKSPACE_DIR}" "${SIF_PATH_IN_NODE}" \
-  ocrd workspace -d "${WORKSPACE_DIR_IN_DOCKER}" remove-group -r -f "$1" \
-  > "${WORKSPACE_DIR}/remove_file_groups.log" 2>&1
+  REMOVE_FILE_GROUP_COMMAND="${REMOVE_FILE_GROUP_COMMAND//FILE_GROUP_PLACEHOLDER/$1}"
+  eval "$REMOVE_FILE_GROUP_COMMAND"
 }
 
 remove_file_groups_from_workspace() {
@@ -244,7 +282,9 @@ zip_results() {
 # Main loop for workflow job execution
 check_existence_of_paths
 unzip_workflow_job_dir
-transfer_requirements_to_node_storage
+echo ""
+transfer_to_node_storage_processor_models
+transfer_to_node_storage_processor_images
 start_mets_server "$USE_METS_SERVER"
 execute_nextflow_workflow "$USE_METS_SERVER"
 stop_mets_server "$USE_METS_SERVER"
diff --git a/src/utils/operandi_utils/hpc/constants.py b/src/utils/operandi_utils/hpc/constants.py
index 1d7ef807..156cd45a 100644
--- a/src/utils/operandi_utils/hpc/constants.py
+++ b/src/utils/operandi_utils/hpc/constants.py
@@ -68,8 +68,9 @@
 
 HPC_JOB_DEADLINE_TIME_REGULAR = "48:00:00"
 HPC_JOB_DEADLINE_TIME_TEST = "00:30:00"
-HPC_NHR_JOB_DEFAULT_PARTITION = "standard96s:shared"
-HPC_NHR_JOB_TEST_PARTITION = "standard96s:shared"
+# TODO: Use again "standard96s:shared"
+HPC_NHR_JOB_DEFAULT_PARTITION = "standard96:shared"
+HPC_NHR_JOB_TEST_PARTITION = "standard96:shared"
 
 # Check here: https://docs.hpc.gwdg.de/getting_started/transition/index.html
 HPC_JOB_QOS_SHORT = "2h"
diff --git a/src/utils/operandi_utils/hpc/nhr_connector.py b/src/utils/operandi_utils/hpc/nhr_connector.py
index 8d549bd4..6ea693bf 100644
--- a/src/utils/operandi_utils/hpc/nhr_connector.py
+++ b/src/utils/operandi_utils/hpc/nhr_connector.py
@@ -33,9 +33,10 @@ def __init__(
         self._ssh_reconnect_tries = 5
         self._ssh_reconnect_tries_remaining = self._ssh_reconnect_tries
         # TODO: Make the sub cluster options selectable
-        self.project_root_dir = join(HPC_NHR_CLUSTERS["EmmyPhase2"]["scratch-emmy-hdd"], project_env)
-        self.batch_scripts_dir = join(self.project_root_dir, "batch_scripts")
-        self.slurm_workspaces_dir = join(self.project_root_dir, "slurm_workspaces")
+        self.project_root_dir: str = HPC_NHR_CLUSTERS["EmmyPhase2"]["scratch-emmy-hdd"]
+        self.project_root_dir_with_env: str = join(self.project_root_dir, project_env)
+        self.batch_scripts_dir: str = join(self.project_root_dir, project_env, "batch_scripts")
+        self.slurm_workspaces_dir: str = join(self.project_root_dir, project_env, "slurm_workspaces")
 
     @property
     def ssh_client(self):
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index d450cbc6..90f4c4c0 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -1,5 +1,6 @@
 from json import dumps
 from logging import getLogger
+from os.path import join
 from pathlib import Path
 from time import sleep
 
@@ -10,6 +11,7 @@
 )
 from .nhr_connector import NHRConnector
 
+
 class NHRExecutor(NHRConnector):
     def __init__(self) -> None:
         logger = getLogger(name=self.__class__.__name__)
@@ -58,19 +60,38 @@ def trigger_slurm_job(
             "qos": qos,
             "batch_script_path": HPC_BATCH_SUBMIT_WORKFLOW_JOB
         }
+
+        hpc_workflow_job_dir = join(self.slurm_workspaces_dir, workflow_job_id)
+        hpc_nf_script_path = join(self.slurm_workspaces_dir, workflow_job_id, nextflow_script_id)
+        hpc_workspace_dir = join(self.slurm_workspaces_dir, workflow_job_id, workspace_id)
+
+        # NODE_PATH_OCRD_MODELS_PLACEHOLDER and NODE_PATH_SIF_PLACEHOLDER are just placeholders to be replaced
+        # with actual paths that are dynamically allocated inside the node that runs the HPC slurm job
+        ph_node_dir_ocrd_models = "PH_NODE_DIR_OCRD_MODELS"
+        ph_node_sif_path_ocrd_all = "PH_NODE_SIF_PATH_OCRD_ALL"
+
+        nf_run_command = self.cmd_nextflow_run(
+            hpc_nf_script_path=hpc_nf_script_path, hpc_ws_dir=hpc_workspace_dir,
+            bind_ocrd_models=f"{ph_node_dir_ocrd_models}/ocrd-resources:/usr/local/share/ocrd-resources",
+            ph_sif_ocrd_all=ph_node_sif_path_ocrd_all, input_file_grp=input_file_grp, mets_basename=mets_basename,
+            use_mets_server=use_mets_server, ws_pages_amount=ws_pages_amount, cpus=cpus, ram=ram, forks=nf_process_forks
+        )
+
         regular_args = {
+            "project_base_dir": self.project_root_dir,
             "scratch_base_dir": self.slurm_workspaces_dir,
+            "ocrd_processor_images": "ocrd_all_maximum_image.sif,dummy1.sif,dummy2.sif,dummy3.sif",
             "workflow_job_id": workflow_job_id,
-            "nextflow_script_id": nextflow_script_id,
-            "input_file_group": input_file_grp,
             "workspace_id": workspace_id,
-            "mets_basename": mets_basename,
-            "cpus": cpus,
-            "ram": ram,
-            "nf_process_forks": nf_process_forks,
-            "ws_pages_amount": ws_pages_amount,
             "use_mets_server_bash_flag": use_mets_server_bash_flag,
-            "file_groups_to_remove": file_groups_to_remove
+            "file_groups_to_remove": file_groups_to_remove,
+            "hpc_workflow_job_dir": hpc_workflow_job_dir,
+            "hpc_workspace_dir": hpc_workspace_dir,
+            "nf_run_command": nf_run_command,
+            "start_mets_server_command": self.cmd_core_start_mets_server(hpc_workspace_dir, ph_node_sif_path_ocrd_all),
+            "stop_mets_server_command": self.cmd_core_stop_mets_server(hpc_workspace_dir, ph_node_sif_path_ocrd_all),
+            "list_file_groups_command": self.cmd_core_list_file_groups(hpc_workspace_dir, ph_node_sif_path_ocrd_all),
+            "remove_file_group_command": self.cmd_core_remove_file_group(hpc_workspace_dir, ph_node_sif_path_ocrd_all)
         }
         command += f" '{dumps(sbatch_args)}' '{dumps(regular_args)}'"
 
@@ -149,3 +170,52 @@ def poll_till_end_slurm_job_state(self, slurm_job_id: str, interval: int = 5, ti
         # Timeout reached
         self.logger.info("Polling slurm job status timeout reached")
         return False
+
+    @staticmethod
+    def cmd_nextflow_run(
+        hpc_nf_script_path: str, hpc_ws_dir: str, bind_ocrd_models: str, ph_sif_ocrd_all: str, input_file_grp: str,
+        mets_basename: str, use_mets_server: bool, ws_pages_amount: int, cpus: int, ram: int, forks: int
+    ) -> str:
+        apptainer_cmd = f"apptainer exec --bind {hpc_ws_dir}:/ws_data --bind {bind_ocrd_models}"
+        apptainer_cmd += f" --env OCRD_METS_CACHING=false {ph_sif_ocrd_all}"
+
+        nf_run_command = f"nextflow run {hpc_nf_script_path} -ansi-log false -with-report"
+        nf_run_command += f" --input_file_group {input_file_grp}"
+        nf_run_command += f" --mets /ws_data/{mets_basename}"
+        if use_mets_server:
+            nf_run_command += f" --mets_socket /ws_data/mets_server.sock"
+        nf_run_command += f" --workspace_dir /ws_data"
+        nf_run_command += f" --pages {ws_pages_amount}"
+        # Command wrapper placeholder. Each occurrence is replaced with a single quote ' to avoid json parsing errors
+        ph_cmd_wrapper = "PH_CMD_WRAPPER"
+        nf_run_command += f" --singularity_wrapper {ph_cmd_wrapper}{apptainer_cmd}{ph_cmd_wrapper}"
+        nf_run_command += f" --cpus {cpus}"
+        nf_run_command += f" --ram {ram}"
+        nf_run_command += f" --forks {forks}"
+        return nf_run_command
+
+    @staticmethod
+    def cmd_core_start_mets_server(hpc_ws_dir: str, ph_sif_core: str) -> str:
+        command = f"apptainer exec --bind {hpc_ws_dir}:/ws_data {ph_sif_core}"
+        command += f" ocrd workspace -d /ws_data -U /ws_data/mets_server.sock server start"
+        command += f" > {hpc_ws_dir}/mets_server.log 2>&1 &"
+        return command
+
+    @staticmethod
+    def cmd_core_stop_mets_server(hpc_ws_dir: str, ph_sif_core: str) -> str:
+        command = f"apptainer exec --bind {hpc_ws_dir}:/ws_data {ph_sif_core}"
+        command += " ocrd workspace -d /ws_data -U /ws_data/mets_server.sock server stop"
+        return command
+
+    @staticmethod
+    def cmd_core_list_file_groups(hpc_ws_dir: str, ph_sif_core: str) -> str:
+        command = f"apptainer exec --bind {hpc_ws_dir}:/ws_data {ph_sif_core}"
+        command += " ocrd workspace -d /ws_data list-group"
+        return command
+
+    @staticmethod
+    def cmd_core_remove_file_group(hpc_ws_dir: str, ph_sif_core: str) -> str:
+        command = f"apptainer exec --bind {hpc_ws_dir}:/ws_data {ph_sif_core}"
+        command += " ocrd workspace -d /ws_data remove-group -r -f FILE_GROUP_PLACEHOLDER"
+        command += f" > {hpc_ws_dir}/remove_file_groups.log 2>&1"
+        return command
diff --git a/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py b/tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py
similarity index 100%
rename from tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
rename to tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py
diff --git a/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py b/tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py
similarity index 100%
rename from tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
rename to tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py

From 7317db34026c5d535b905c0ebf6e322dffe0174f Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Tue, 26 Nov 2024 14:58:35 +0100
Subject: [PATCH 04/16] add executable to image mapping

---
 src/utils/operandi_utils/constants.py         | 75 +++++++++++++++++++
 .../batch_check_ocrd_all_version.sh           |  0
 .../batch_create_ocrd_all_maximum_sif.sh      |  2 +-
 .../batch_create_ocrd_slim_sif_images.sh      | 64 ++++++++++++++++
 .../batch_download_ocrd_all_models.sh         |  2 +-
 .../wrapper_check_workflow_job_status.sh      |  0
 .../wrapper_submit_workflow_job.sh            |  0
 7 files changed, 141 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh
 create mode 100755 src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh
 mode change 100644 => 100755 src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
 mode change 100644 => 100755 src/utils/operandi_utils/hpc/batch_scripts/wrapper_check_workflow_job_status.sh
 mode change 100644 => 100755 src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh

diff --git a/src/utils/operandi_utils/constants.py b/src/utils/operandi_utils/constants.py
index 542fcdaf..57fe6e17 100644
--- a/src/utils/operandi_utils/constants.py
+++ b/src/utils/operandi_utils/constants.py
@@ -165,3 +165,78 @@ class StateWorkspace(str, Enum):
     TRANSFERRING_TO_HPC = "TRANSFERRING_TO_HPC"
     TRANSFERRING_FROM_HPC = "TRANSFERRING_FROM_HPC"
     UNSET = "UNSET"
+
+# TODO: Find a more optimal way of achieving this dynamically
+OCRD_PROCESSOR_NAME_TO_IMAGE = {
+    "ocrd": "ocrd_core.sif",
+    "ocrd-tesserocr-crop": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-deskew": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-recognize": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-segment": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-segment-line": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-segment-region": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-segment-table": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-segment-word": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-fontshape": "ocrd_tesserocr.sif",
+    "ocrd-tesserocr-binarize": "ocrd_tesserocr.sif",
+    "ocrd-cis-ocropy-binarize": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-denoise": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-deskew": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-dewarp": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-segment": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-resegment": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-clip": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-recognize": "ocrd_cis.sif",
+    "ocrd-cis-ocropy-train": "ocrd_cis.sif",
+    "ocrd-cis-align": "ocrd_cis.sif",
+    "ocrd-cis-postcorrect": "ocrd_cis.sif",
+    "ocrd-kraken-recognize": "ocrd_kraken.sif",
+    "ocrd-kraken-segment": "ocrd_kraken.sif",
+    "ocrd-kraken-binarize": "ocrd_kraken.sif",
+    "ocrd-preprocess-image": "ocrd_wrap.sif",
+    "ocrd-skimage-normalize": "ocrd_wrap.sif",
+    "ocrd-skimage-binarize": "ocrd_wrap.sif",
+    "ocrd-skimage-denoise": "ocrd_wrap.sif",
+    "ocrd-skimage-denoise-raw": "ocrd_wrap.sif",
+    "ocrd-calamari-recognize": "ocrd_calamari.sif",
+    "ocrd-olena-binarize": "ocrd_olena.sif",
+    "ocrd-dinglehopper": "ocrd_dinglehopper.sif",
+    "ocrd-eynollah-segment": "ocrd_eynollah.sif",
+    "ocrd-fileformat-transform": "ocrd_fileformat.sif",
+    "ocrd-nmalign-merge": "ocrd_nmalign.sif",
+    "ocrd-segment-extract-glyphs": "ocrd_segment.sif",
+    "ocrd-segment-extract-lines": "ocrd_segment.sif",
+    "ocrd-segment-extract-pages": "ocrd_segment.sif",
+    "ocrd-segment-extract-regions": "ocrd_segment.sif",
+    "ocrd-segment-extract-words": "ocrd_segment.sif",
+    "ocrd-segment-from-coco": "ocrd_segment.sif",
+    "ocrd-segment-from-masks": "ocrd_segment.sif",
+    "ocrd-segment-project": "ocrd_segment.sif",
+    "ocrd-segment-repair": "ocrd_segment.sif",
+    "ocrd-segment-replace-original": "ocrd_segment.sif",
+    "ocrd-segment-replace-page": "ocrd_segment.sif",
+    "ocrd-segment-replace-text": "ocrd_segment.sif",
+    "ocrd-segment-evaluate": "ocrd_segment.sif",
+    "ocrd-anybaseocr-dewarp": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-crop": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-binarize": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-layout-analysis": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-textline": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-tiseg": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-block-segmentation": "ocrd_anybaseocr.sif",
+    "ocrd-anybaseocr-deskew": "ocrd_anybaseocr.sif",
+    "ocrd-sbb-binarize": "ocrd_sbb_binarization.sif",
+    "ocrd-detectron2-segment": "ocrd_detectron2.sif",
+    "ocrd-froc": "ocrd_froc.sif",
+    "ocrd-pagetopdf": "ocrd_pagetopdf.sif",
+    "ocrd-keraslm-rate": "ocrd_keraslm.sif",
+    "ocrd-docstruct": "ocrd_docstruct.sif",
+    "ocrd-doxa-binarize": "ocrd_doxa.sif",
+    "ocrd-im6convert": "ocrd_im6convert.sif",
+    "ocrd-olahd-client": "ocrd_olahd-client.sif",
+    "ocrd-cor-asv-ann-mark": "ocrd_cor-asv-ann.sif",
+    "ocrd-cor-asv-ann-align": "ocrd_cor-asv-ann.sif",
+    "ocrd-cor-asv-ann-evaluate": "ocrd_cor-asv-ann.sif",
+    "ocrd-cor-asv-ann-join": "ocrd_cor-asv-ann.sif",
+    "ocrd-cor-asv-ann-process": "ocrd_cor-asv-ann.sif"
+}
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_check_ocrd_all_version.sh
old mode 100644
new mode 100755
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh
index 7ac3f522..d5e68d31 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_all_maximum_sif.sh
@@ -11,7 +11,7 @@ module purge
 module load apptainer
 
 hostname
-/opt/slurm/etc/scripts/misc/slurm_resources
+# /opt/slurm/etc/scripts/misc/slurm_resources
 
 APPTAINER_TMPDIR="$LOCAL_TMPDIR"
 APPTAINER_CACHE_DIR="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr"
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh
new file mode 100755
index 00000000..c750316a
--- /dev/null
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh
@@ -0,0 +1,64 @@
+#!/bin/bash
+#SBATCH --partition standard96s:shared
+#SBATCH --time 4:00:00
+#SBATCH --output create_ocrd_slim_sif_images_job-%J.txt
+#SBATCH --cpus-per-task 16
+#SBATCH --mem 64G
+
+set -e
+
+module purge
+module load apptainer
+
+hostname
+# /opt/slurm/etc/scripts/misc/slurm_resources
+
+APPTAINER_TMPDIR="$LOCAL_TMPDIR"
+APPTAINER_CACHE_DIR="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_processor_sifs_tmp"
+
+if [ ! -d "${APPTAINER_CACHE_DIR}" ]; then
+  echo "Creating non-existing APPTAINER_CACHE_DIR folder"
+  mkdir -p "${APPTAINER_CACHE_DIR}"
+fi
+
+cd "${APPTAINER_CACHE_DIR}" || exit
+# apptainer build --disable-cache "ocrd_all_maximum_image_new.sif" "docker://ocrd/all:latest"
+# apptainer exec "ocrd_all_maximum_image_new.sif" ocrd --version
+
+declare -a images=(
+"core"
+"tesserocr"
+"cis"
+"kraken"
+"wrap"
+"calamari"
+"olena"
+"dinglehopper"
+"eynollah"
+"fileformat"
+"nmalign"
+"segment"
+"anybaseocr"
+"sbb_binarization"
+"detectron2"
+"froc"
+"pagetopdf"
+"keraslm"
+"docstruct"
+"doxa"
+"im6convert"
+"olahd-client"
+"cor-asv-ann"
+)
+
+for image in "${images[@]}"
+do
+    if [ -f "$APPTAINER_CACHE_DIR/ocrd_$image.sif" ]; then
+      echo "Already exists, skipping: $APPTAINER_CACHE_DIR/ocrd_$image.sif"
+      continue
+    fi
+    echo "Building SIF of $image"
+    apptainer build --disable-cache "ocrd_$image.sif" "docker://ocrd/$image:latest"
+    echo "Building complete: $APPTAINER_CACHE_DIR/ocrd_$image.sif"
+    echo ""
+done
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
old mode 100644
new mode 100755
index fffdf2d5..ed2b7a88
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_download_ocrd_all_models.sh
@@ -11,7 +11,7 @@ module purge
 module load apptainer
 
 hostname
-/opt/slurm/etc/scripts/misc/slurm_resources
+# /opt/slurm/etc/scripts/misc/slurm_resources
 
 # This sif file is generated with another batch script
 SIF_PATH="/mnt/lustre-emmy-hdd/projects/project_pwieder_ocr_nhr/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/wrapper_check_workflow_job_status.sh b/src/utils/operandi_utils/hpc/batch_scripts/wrapper_check_workflow_job_status.sh
old mode 100644
new mode 100755
diff --git a/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/wrapper_submit_workflow_job.sh
old mode 100644
new mode 100755

From 26834553266fcb0a02abf3b325f137a9324eb8ab Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Tue, 26 Nov 2024 15:31:01 +0100
Subject: [PATCH 05/16] remove unnecessary dummy images

---
 .../hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh | 7 +++++--
 src/utils/operandi_utils/hpc/nhr_executor.py               | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh
index c750316a..711b264e 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_create_ocrd_slim_sif_images.sh
@@ -40,7 +40,6 @@ declare -a images=(
 "segment"
 "anybaseocr"
 "sbb_binarization"
-"detectron2"
 "froc"
 "pagetopdf"
 "keraslm"
@@ -48,6 +47,7 @@ declare -a images=(
 "doxa"
 "im6convert"
 "olahd-client"
+"detectron2"
 "cor-asv-ann"
 )
 
@@ -59,6 +59,9 @@ do
     fi
     echo "Building SIF of $image"
     apptainer build --disable-cache "ocrd_$image.sif" "docker://ocrd/$image:latest"
-    echo "Building complete: $APPTAINER_CACHE_DIR/ocrd_$image.sif"
+    case $? in
+      0) echo "Building complete: $APPTAINER_CACHE_DIR/ocrd_$image.sif" ;;
+      *) echo "Building failed, error code: $?" >&2 ;;
+    esac
     echo ""
 done
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index 90f4c4c0..1684dc9b 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -80,7 +80,7 @@ def trigger_slurm_job(
         regular_args = {
             "project_base_dir": self.project_root_dir,
             "scratch_base_dir": self.slurm_workspaces_dir,
-            "ocrd_processor_images": "ocrd_all_maximum_image.sif,dummy1.sif,dummy2.sif,dummy3.sif",
+            "ocrd_processor_images": "ocrd_all_maximum_image.sif",
             "workflow_job_id": workflow_job_id,
             "workspace_id": workspace_id,
             "use_mets_server_bash_flag": use_mets_server_bash_flag,

From 1f0e1ee1edc6df905f529248d58a22a4ec27e329 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Tue, 26 Nov 2024 17:05:29 +0100
Subject: [PATCH 06/16] OtoN: assigns different wrappers per step

---
 src/utils/operandi_utils/oton/constants.py    | 35 ++++--------
 .../operandi_utils/oton/nf_block_process.py   |  7 ++-
 .../operandi_utils/oton/nf_block_workflow.py  |  6 +-
 .../operandi_utils/oton/nf_file_executable.py | 55 ++++++++++---------
 .../oton/process_call_arguments.py            | 14 ++---
 tests/assets/oton/constants.py                | 10 +++-
 .../oton/test_output_nextflow1_apptainer.nf   | 34 +++++++-----
 ...test_output_nextflow1_apptainer_with_MS.nf | 28 ++++++----
 .../oton/test_output_nextflow1_docker.nf      | 34 +++++++-----
 .../test_output_nextflow1_docker_with_MS.nf   | 28 ++++++----
 .../oton/test_output_nextflow1_local.nf       |  8 +++
 .../test_output_nextflow1_local_with_MS.nf    |  8 +++
 tests/assets/oton/test_output_nextflow2.nf    |  7 +++
 tests/assets/oton/test_output_nextflow3.nf    |  3 +
 tests/assets/oton/test_output_nextflow4.nf    | 13 +++++
 tests/tests_utils/test_2_oton/assert_utils.py | 12 ++--
 ...nhr_executor.py => test_1_nhr_executor.py} |  0
 ...nhr_transfer.py => test_2_nhr_transfer.py} |  0
 18 files changed, 184 insertions(+), 118 deletions(-)
 rename tests/tests_utils/test_3_hpc/{_test_1_nhr_executor.py => test_1_nhr_executor.py} (100%)
 rename tests/tests_utils/test_3_hpc/{_test_2_nhr_transfer.py => test_2_nhr_transfer.py} (100%)

diff --git a/src/utils/operandi_utils/oton/constants.py b/src/utils/operandi_utils/oton/constants.py
index c743bd5d..80750029 100644
--- a/src/utils/operandi_utils/oton/constants.py
+++ b/src/utils/operandi_utils/oton/constants.py
@@ -3,6 +3,15 @@
 from pkg_resources import resource_filename
 from operandi_utils.constants import OPERANDI_VERSION
 
+BS: str = '{}'
+SPACES = '    '
+CONST_DIR_IN: str = 'input_group'
+CONST_DIR_OUT: str = 'output_group'
+CONST_PAGE_RANGE: str = 'page_range'
+CONST_METS_PATH: str = 'mets_path'
+CONST_METS_SOCKET_PATH: str = 'mets_socket_path'
+CONST_WORKSPACE_DIR: str = 'workspace_dir'
+
 OCRD_ALL_JSON_FILE = resource_filename(__name__, 'ocrd_all_tool.json')
 with open(OCRD_ALL_JSON_FILE) as f:
     OCRD_ALL_JSON = load(f)
@@ -10,11 +19,12 @@
 OTON_LOG_LEVEL = environ.get("OTON_LOG_LEVEL", "INFO")
 OTON_LOG_FORMAT = '%(asctime)s %(levelname)s %(name)s:%(funcName)s: %(lineno)s: %(message)s'
 
+PARAMS_KEY_ENV_WRAPPER_CMD_CORE: str = 'params.env_wrapper_cmd_core'
+PARAMS_KEY_ENV_WRAPPER_CMD_STEP: str = 'params.env_wrapper_cmd_step'
 PARAMS_KEY_INPUT_FILE_GRP: str = 'params.input_file_group'
 PARAMS_KEY_METS_PATH: str = 'params.mets_path'
 PARAMS_KEY_METS_SOCKET_PATH: str = 'params.mets_socket_path'
 PARAMS_KEY_WORKSPACE_DIR: str = 'params.workspace_dir'
-PARAMS_KEY_ENV_WRAPPER_CMD: str = 'params.env_wrapper_cmd'
 PARAMS_KEY_PAGES: str = 'params.pages'
 PARAMS_KEY_CPUS: str = 'params.cpus'
 PARAMS_KEY_RAM: str = 'params.ram'
@@ -26,7 +36,7 @@
 REPR_METS_PATH: str = f"""{PARAMS_KEY_METS_PATH} = "null\""""
 REPR_METS_SOCKET_PATH: str = f"""{PARAMS_KEY_METS_SOCKET_PATH} = "null\""""
 REPR_WORKSPACE_DIR: str = f"""{PARAMS_KEY_WORKSPACE_DIR} = "null\""""
-REPR_ENV_WRAPPER_CMD: str = f"""{PARAMS_KEY_ENV_WRAPPER_CMD} = "null\""""
+REPR_ENV_WRAPPER_CMD_CORE: str = f"""{PARAMS_KEY_ENV_WRAPPER_CMD_CORE} = "null\""""
 REPR_PAGES: str = f"""{PARAMS_KEY_PAGES} = "null\""""
 REPR_CPUS: str = f"""{PARAMS_KEY_CPUS} = "null\""""
 REPR_RAM: str = f"""{PARAMS_KEY_RAM} = "null\""""
@@ -35,25 +45,4 @@
 REPR_CPUS_PER_FORK: str = f"""{PARAMS_KEY_CPUS_PER_FORK} = ({PARAMS_KEY_CPUS}.toInteger() / {PARAMS_KEY_FORKS}.toInteger()).intValue()"""
 REPR_RAM_PER_FORK: str = f"""{PARAMS_KEY_RAM_PER_FORK} = sprintf("%dGB", ({PARAMS_KEY_RAM}.toInteger() / {PARAMS_KEY_FORKS}.toInteger()).intValue())"""
 
-DIR_IN: str = 'input_group'
-DIR_OUT: str = 'output_group'
-PAGE_RANGE: str = 'page_range'
-METS_PATH: str = 'mets_path'
-METS_SOCKET_PATH: str = 'mets_socket_path'
-WORKSPACE_DIR: str = 'workspace_dir'
-
-# Placeholders
-BS: str = '{}'
-PH_ENV_WRAPPER_CMD: str = f'${BS[0]}{PARAMS_KEY_ENV_WRAPPER_CMD}{BS[1]}'
-PH_DIR_IN: str = f'${BS[0]}{DIR_IN}{BS[1]}'
-PH_DIR_OUT: str = f'${BS[0]}{DIR_OUT}{BS[1]}'
-PH_PAGE_RANGE: str = f'${BS[0]}{PAGE_RANGE}{BS[1]}'
-PH_WORKSPACE_DIR: str = f'${BS[0]}{WORKSPACE_DIR}{BS[1]}'
-PH_METS_PATH: str = f'${BS[0]}{METS_PATH}{BS[1]}'
-PH_METS_SOCKET_PATH: str = f'${BS[0]}{METS_SOCKET_PATH}{BS[1]}'
-PH_PARAMS_FORKS: str = f'${BS[0]}{PARAMS_KEY_FORKS}{BS[1]}'
-PH_PARAMS_METS_PATH: str = f'${BS[0]}{PARAMS_KEY_METS_PATH}{BS[1]}'
-PH_PARAMS_WORKSPACE_DIR: str = f'${BS[0]}{PARAMS_KEY_WORKSPACE_DIR}{BS[1]}'
-SPACES = '    '
-
 WORKFLOW_COMMENT = f"// This workflow was automatically generated by the v{OPERANDI_VERSION} operandi_utils.oton module"
diff --git a/src/utils/operandi_utils/oton/nf_block_process.py b/src/utils/operandi_utils/oton/nf_block_process.py
index f1d20991..2f1cb832 100644
--- a/src/utils/operandi_utils/oton/nf_block_process.py
+++ b/src/utils/operandi_utils/oton/nf_block_process.py
@@ -1,16 +1,17 @@
 from logging import getLevelName, getLogger
 from operandi_utils.oton.ocrd_validator import ProcessorCallArguments
-from operandi_utils.oton.constants import OTON_LOG_LEVEL, PH_ENV_WRAPPER_CMD, SPACES
+from operandi_utils.oton.constants import BS, OTON_LOG_LEVEL, PARAMS_KEY_ENV_WRAPPER_CMD_STEP, SPACES
 
 
 class NextflowBlockProcess:
     def __init__(self, processor_call_arguments: ProcessorCallArguments, index_pos: int, env_wrapper: bool = False):
         self.logger = getLogger(__name__)
         self.logger.setLevel(getLevelName(OTON_LOG_LEVEL))
+        self.index_pos = str(index_pos)
 
         self.processor_call_arguments: ProcessorCallArguments = processor_call_arguments
         self.env_wrapper: bool = env_wrapper
-        self.nf_process_name: str = processor_call_arguments.executable.replace('-', '_') + "_" + str(index_pos)
+        self.nf_process_name: str = processor_call_arguments.executable.replace('-', '_') + f"_{self.index_pos}"
         self.directives = {}
         self.input_params = {}
         self.output_params = {}
@@ -61,7 +62,7 @@ def dump_script(self, local_script: bool = False) -> str:
         dump += f'{SPACES}{SPACES}"""\n'
         dump += f'{SPACES}{SPACES}'
         if self.env_wrapper:
-            dump += f'{PH_ENV_WRAPPER_CMD} '
+            dump += f'${BS[0]}{PARAMS_KEY_ENV_WRAPPER_CMD_STEP}{self.index_pos}{BS[1]} '
         dump += f'{self.ocrd_command_bash_placeholders}\n'
         dump += f'{SPACES}{SPACES}"""\n'
         return dump
diff --git a/src/utils/operandi_utils/oton/nf_block_workflow.py b/src/utils/operandi_utils/oton/nf_block_workflow.py
index f73041fd..f6d17374 100644
--- a/src/utils/operandi_utils/oton/nf_block_workflow.py
+++ b/src/utils/operandi_utils/oton/nf_block_workflow.py
@@ -1,11 +1,7 @@
 from logging import getLevelName, getLogger
 from typing import List
 from operandi_utils.oton.constants import (
-    OTON_LOG_LEVEL,
-    PARAMS_KEY_WORKSPACE_DIR,
-    PARAMS_KEY_INPUT_FILE_GRP,
-    PARAMS_KEY_FORKS,
-    SPACES
+    OTON_LOG_LEVEL, PARAMS_KEY_WORKSPACE_DIR, PARAMS_KEY_INPUT_FILE_GRP, PARAMS_KEY_FORKS, SPACES
 )
 from operandi_utils.oton.nf_block_process import NextflowBlockProcess
 
diff --git a/src/utils/operandi_utils/oton/nf_file_executable.py b/src/utils/operandi_utils/oton/nf_file_executable.py
index 6007fc0b..43a94744 100644
--- a/src/utils/operandi_utils/oton/nf_file_executable.py
+++ b/src/utils/operandi_utils/oton/nf_file_executable.py
@@ -3,15 +3,17 @@
 
 from operandi_utils.oton.ocrd_validator import ProcessorCallArguments
 from operandi_utils.oton.constants import (
-    DIR_IN, DIR_OUT, PAGE_RANGE, METS_PATH, WORKSPACE_DIR,
+    BS, CONST_DIR_IN, CONST_DIR_OUT, CONST_PAGE_RANGE, CONST_METS_PATH, CONST_WORKSPACE_DIR,
     OTON_LOG_LEVEL,
     PARAMS_KEY_INPUT_FILE_GRP,
-    PH_PARAMS_WORKSPACE_DIR, PH_PARAMS_METS_PATH, PH_PARAMS_FORKS,
-    PH_ENV_WRAPPER_CMD,
+    PARAMS_KEY_METS_PATH,
+    PARAMS_KEY_WORKSPACE_DIR,
+    PARAMS_KEY_ENV_WRAPPER_CMD_CORE,
+    PARAMS_KEY_ENV_WRAPPER_CMD_STEP,
     PARAMS_KEY_FORKS,
     PARAMS_KEY_CPUS_PER_FORK,
     PARAMS_KEY_RAM_PER_FORK,
-    REPR_ENV_WRAPPER_CMD,
+    REPR_ENV_WRAPPER_CMD_CORE,
     REPR_INPUT_FILE_GRP,
     REPR_METS_PATH,
     REPR_METS_SOCKET_PATH,
@@ -60,16 +62,14 @@ def build_parameters(self, environment: str, with_mets_server: bool):
             self.nf_lines_parameters.append(REPR_FORKS_NULL)
         if environment == "docker":
             self.nf_lines_parameters.append(REPR_FORKS_NULL)
-            self.nf_lines_parameters.append(REPR_ENV_WRAPPER_CMD)
+            self.nf_lines_parameters.append(REPR_ENV_WRAPPER_CMD_CORE)
         if environment == "apptainer":
             self.nf_lines_parameters.append(REPR_CPUS)
             self.nf_lines_parameters.append(REPR_RAM)
             self.nf_lines_parameters.append(REPR_FORKS)
             self.nf_lines_parameters.append(REPR_CPUS_PER_FORK)
             self.nf_lines_parameters.append(REPR_RAM_PER_FORK)
-            self.nf_lines_parameters.append(REPR_ENV_WRAPPER_CMD)
-
-        self.nf_lines_parameters.append('')
+            self.nf_lines_parameters.append(REPR_ENV_WRAPPER_CMD_CORE)
 
     # TODO: Refactor later
     def build_split_page_ranges_process(self, environment: str, with_mets_server: bool) -> NextflowBlockProcess:
@@ -91,24 +91,24 @@ def build_split_page_ranges_process(self, environment: str, with_mets_server: bo
 
         PH_RANGE_MULTIPLIER = '${range_multiplier}'
         bash_cmd_ocrd_ws = (
-            f"ocrd workspace -d {PH_PARAMS_WORKSPACE_DIR} list-page -f comma-separated "
-            f"-D {PH_PARAMS_FORKS} -C {PH_RANGE_MULTIPLIER}"
+            f"ocrd workspace -d ${BS[0]}{PARAMS_KEY_WORKSPACE_DIR}{BS[1]} list-page -f comma-separated "
+            f"-D ${BS[0]}{PARAMS_KEY_FORKS}{BS[1]} -C {PH_RANGE_MULTIPLIER}"
         )
-        bash_cmd_copy_mets_chunk = f"cp -p {PH_PARAMS_METS_PATH} \\$mets_file_chunk"
+        bash_cmd_copy_mets_chunk = f"cp -p ${BS[0]}{PARAMS_KEY_METS_PATH}{BS[1]} \\$mets_file_chunk"
 
         script = f'{SPACES}{SPACES}"""\n{SPACES}{SPACES}'
         script += f"current_range_pages=\\$("
         if environment == "apptainer" or environment == "docker":
-            script += f"{PH_ENV_WRAPPER_CMD} "
+            script += f"${BS[0]}{PARAMS_KEY_ENV_WRAPPER_CMD_CORE}{BS[1]} "
         script += f"{bash_cmd_ocrd_ws})\n"
         script += f'{SPACES}{SPACES}echo "Current range is: \\$current_range_pages"\n'
 
         if not with_mets_server:
-            script += f"{SPACES}{SPACES}mets_file_chunk=\\$(echo {PH_PARAMS_WORKSPACE_DIR}/mets_{PH_RANGE_MULTIPLIER}.xml)\n"
+            script += f"{SPACES}{SPACES}mets_file_chunk=\\$(echo ${BS[0]}{PARAMS_KEY_WORKSPACE_DIR}{BS[1]}/mets_{PH_RANGE_MULTIPLIER}.xml)\n"
             script += f'{SPACES}{SPACES}echo "Mets file chunk path: \\$mets_file_chunk"\n'
             script += f"{SPACES}{SPACES}\\$("
             if environment == "apptainer" or environment == "docker":
-                script += f"{PH_ENV_WRAPPER_CMD} "
+                script += f"${BS[0]}{PARAMS_KEY_ENV_WRAPPER_CMD_CORE}{BS[1]} "
             script += f"{bash_cmd_copy_mets_chunk})\n"
         script += f'{SPACES}{SPACES}"""\n'
         block.script = script
@@ -135,15 +135,16 @@ def build_merge_mets_process(self, environment: str) -> NextflowBlockProcess:
         PH_METS_FILE_CHUNK = "${mets_file_chunk}"
         PH_PAGE_RANGE = "${page_range}"
         bash_cmd_ocrd_ws = (
-            f"ocrd workspace -d {PH_PARAMS_WORKSPACE_DIR} merge --force --no-copy-files {PH_METS_FILE_CHUNK} "
+            f"ocrd workspace -d ${BS[0]}{PARAMS_KEY_WORKSPACE_DIR}{BS[1]} "
+            f"merge --force --no-copy-files {PH_METS_FILE_CHUNK} "
             f"--page-id {PH_PAGE_RANGE}"
         )
         script = f'{SPACES}{SPACES}"""\n{SPACES}{SPACES}'
         if environment == "apptainer" or environment == "docker":
-            script += f"{PH_ENV_WRAPPER_CMD} "
+            script += f"${BS[0]}{PARAMS_KEY_ENV_WRAPPER_CMD_CORE}{BS[1]} "
         script += f"{bash_cmd_ocrd_ws}\n{SPACES}{SPACES}"
         if environment == "apptainer" or environment == "docker":
-            script += f"{PH_ENV_WRAPPER_CMD} "
+            script += f"${BS[0]}{PARAMS_KEY_ENV_WRAPPER_CMD_CORE}{BS[1]} "
         script += f"rm {PH_METS_FILE_CHUNK}\n"
         script += f'{SPACES}{SPACES}"""\n'
         block.script = script
@@ -168,15 +169,16 @@ def build_nextflow_processes(
                 nf_process_block.add_directive(directive='memory', value=PARAMS_KEY_RAM_PER_FORK)
 
             # Add Nextflow process parameters
-            nf_process_block.add_parameter_input(parameter=METS_PATH, parameter_type='val')
-            nf_process_block.add_parameter_input(parameter=PAGE_RANGE, parameter_type='val')
-            nf_process_block.add_parameter_input(parameter=WORKSPACE_DIR, parameter_type='val')
-            nf_process_block.add_parameter_input(parameter=DIR_IN, parameter_type='val')
-            nf_process_block.add_parameter_input(parameter=DIR_OUT, parameter_type='val')
-
-            nf_process_block.add_parameter_output(parameter=METS_PATH, parameter_type='val')
-            nf_process_block.add_parameter_output(parameter=PAGE_RANGE, parameter_type='val')
-            nf_process_block.add_parameter_output(parameter=WORKSPACE_DIR, parameter_type='val')
+            nf_process_block.add_parameter_input(parameter=CONST_METS_PATH, parameter_type='val')
+            nf_process_block.add_parameter_input(parameter=CONST_PAGE_RANGE, parameter_type='val')
+            nf_process_block.add_parameter_input(parameter=CONST_WORKSPACE_DIR, parameter_type='val')
+            nf_process_block.add_parameter_input(parameter=CONST_DIR_IN, parameter_type='val')
+            nf_process_block.add_parameter_input(parameter=CONST_DIR_OUT, parameter_type='val')
+
+            nf_process_block.add_parameter_output(parameter=CONST_METS_PATH, parameter_type='val')
+            nf_process_block.add_parameter_output(parameter=CONST_PAGE_RANGE, parameter_type='val')
+            nf_process_block.add_parameter_output(parameter=CONST_WORKSPACE_DIR, parameter_type='val')
+            self.nf_lines_parameters.append(f'{PARAMS_KEY_ENV_WRAPPER_CMD_STEP}{index} = "null"')
             self.nf_blocks_process.append(nf_process_block)
             index += 1
 
@@ -208,6 +210,7 @@ def produce_nextflow_file(self, output_path: str, environment: str, with_mets_se
             nextflow_file.write(f"{WORKFLOW_COMMENT}\n")
             for nextflow_line in self.nf_lines_parameters:
                 nextflow_file.write(f'{nextflow_line}\n')
+            nextflow_file.write("\n")
             nextflow_file.write(f'{self.nf_process_split_range.file_representation(local_script=True)}\n')
             for block in self.nf_blocks_process:
                 nextflow_file.write(f'{block.file_representation(local_script=False)}\n')
diff --git a/src/utils/operandi_utils/oton/process_call_arguments.py b/src/utils/operandi_utils/oton/process_call_arguments.py
index d9eb8005..e1f7600e 100644
--- a/src/utils/operandi_utils/oton/process_call_arguments.py
+++ b/src/utils/operandi_utils/oton/process_call_arguments.py
@@ -2,8 +2,8 @@
 from logging import getLevelName, getLogger
 from typing import Optional
 from operandi_utils.oton.constants import (
-    OCRD_ALL_JSON, OTON_LOG_LEVEL,
-    PH_DIR_IN, PH_DIR_OUT, PH_WORKSPACE_DIR, PH_METS_PATH, PH_METS_SOCKET_PATH, PH_PAGE_RANGE
+    BS, CONST_DIR_IN, CONST_DIR_OUT, CONST_WORKSPACE_DIR, CONST_METS_PATH, CONST_METS_SOCKET_PATH,
+    OCRD_ALL_JSON, OTON_LOG_LEVEL
 )
 
 # This class is based on ocrd.task_sequence.ProcessorTask
@@ -55,11 +55,11 @@ def dump_bash_form_with_placeholders(self):
         dump = ''
         dump += f'{self.executable}'
         if self.mets_socket_path:
-            dump += f' -U {PH_METS_SOCKET_PATH}'
-        dump += f' -w {PH_WORKSPACE_DIR}'
-        dump += f' -m {PH_METS_PATH}'
-        dump += f' -I {PH_DIR_IN}'
-        dump += f' -O {PH_DIR_OUT}'
+            dump += f' -U ${BS[0]}{CONST_METS_SOCKET_PATH}{BS[1]}'
+        dump += f' -w ${BS[0]}{CONST_WORKSPACE_DIR}{BS[1]}'
+        dump += f' -m ${BS[0]}{CONST_METS_PATH}{BS[1]}'
+        dump += f' -I ${BS[0]}{CONST_DIR_IN}{BS[1]}'
+        dump += f' -O ${BS[0]}{CONST_DIR_OUT}{BS[1]}'
         if self.parameters:
             dump += f" -p '{json_dumps(self.parameters)}'"
         return dump
diff --git a/tests/assets/oton/constants.py b/tests/assets/oton/constants.py
index e336d360..91404cda 100644
--- a/tests/assets/oton/constants.py
+++ b/tests/assets/oton/constants.py
@@ -118,7 +118,10 @@
 
 PARAMETERS_DOCKER = [
     'params.forks = "4"',
-    'params.env_wrapper_cmd = "null"'
+    'params.env_wrapper_cmd_core = "null"',
+    'params.env_wrapper_cmd_step0 = "null"',
+    'params.env_wrapper_cmd_step1 = "null"',
+    'params.env_wrapper_cmd_step2 = "null"',
 ]
 
 PARAMETERS_APPTAINER = [
@@ -127,5 +130,8 @@
     'params.forks = params.cpus',
     'params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()',
     'params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())',
-    'params.env_wrapper_cmd = "null"'
+    'params.env_wrapper_cmd_core = "null"',
+    'params.env_wrapper_cmd_step0 = "null"',
+    'params.env_wrapper_cmd_step1 = "null"',
+    'params.env_wrapper_cmd_step2 = "null"',
 ]
diff --git a/tests/assets/oton/test_output_nextflow1_apptainer.nf b/tests/assets/oton/test_output_nextflow1_apptainer.nf
index b1f6420e..836b69a0 100644
--- a/tests/assets/oton/test_output_nextflow1_apptainer.nf
+++ b/tests/assets/oton/test_output_nextflow1_apptainer.nf
@@ -10,7 +10,15 @@ params.ram = "null"
 params.forks = params.cpus
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-params.env_wrapper_cmd = "null"
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
     debug true
@@ -27,11 +35,11 @@ process split_page_ranges {
 
     script:
         """
-        current_range_pages=\$(${params.env_wrapper_cmd} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
         mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
         echo "Mets file chunk path: \$mets_file_chunk"
-        \$(${params.env_wrapper_cmd} cp -p ${params.mets_path} \$mets_file_chunk)
+        \$(${params.env_wrapper_cmd_core} cp -p ${params.mets_path} \$mets_file_chunk)
         """
 }
 
@@ -55,7 +63,7 @@ process ocrd_cis_ocropy_binarize_0 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -79,7 +87,7 @@ process ocrd_anybaseocr_crop_1 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -103,7 +111,7 @@ process ocrd_skimage_binarize_2 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+        ${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
         """
 }
 
@@ -127,7 +135,7 @@ process ocrd_skimage_denoise_3 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -151,7 +159,7 @@ process ocrd_tesserocr_deskew_4 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
         """
 }
 
@@ -175,7 +183,7 @@ process ocrd_cis_ocropy_segment_5 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -199,7 +207,7 @@ process ocrd_cis_ocropy_dewarp_6 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -223,7 +231,7 @@ process ocrd_calamari_recognize_7 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+        ${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
         """
 }
 
@@ -239,8 +247,8 @@ process merging_mets {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
-        ${params.env_wrapper_cmd} rm ${mets_file_chunk}
+        ${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
+        ${params.env_wrapper_cmd_core} rm ${mets_file_chunk}
         """
 }
 
diff --git a/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf b/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
index 8161c006..ce5de9c7 100644
--- a/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
@@ -11,7 +11,15 @@ params.ram = "null"
 params.forks = params.cpus
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-params.env_wrapper_cmd = "null"
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
     debug true
@@ -27,7 +35,7 @@ process split_page_ranges {
 
     script:
         """
-        current_range_pages=\$(${params.env_wrapper_cmd} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
         """
 }
@@ -52,7 +60,7 @@ process ocrd_cis_ocropy_binarize_0 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -76,7 +84,7 @@ process ocrd_anybaseocr_crop_1 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -100,7 +108,7 @@ process ocrd_skimage_binarize_2 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+        ${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
         """
 }
 
@@ -124,7 +132,7 @@ process ocrd_skimage_denoise_3 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -148,7 +156,7 @@ process ocrd_tesserocr_deskew_4 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
         """
 }
 
@@ -172,7 +180,7 @@ process ocrd_cis_ocropy_segment_5 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -196,7 +204,7 @@ process ocrd_cis_ocropy_dewarp_6 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -220,7 +228,7 @@ process ocrd_calamari_recognize_7 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+        ${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
         """
 }
 
diff --git a/tests/assets/oton/test_output_nextflow1_docker.nf b/tests/assets/oton/test_output_nextflow1_docker.nf
index bbe7888d..aa10c21c 100644
--- a/tests/assets/oton/test_output_nextflow1_docker.nf
+++ b/tests/assets/oton/test_output_nextflow1_docker.nf
@@ -6,7 +6,15 @@ params.mets_path = "null"
 params.workspace_dir = "null"
 params.pages = "null"
 params.forks = "4"
-params.env_wrapper_cmd = "null"
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
     debug true
@@ -21,11 +29,11 @@ process split_page_ranges {
 
     script:
         """
-        current_range_pages=\$(${params.env_wrapper_cmd} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
         mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
         echo "Mets file chunk path: \$mets_file_chunk"
-        \$(${params.env_wrapper_cmd} cp -p ${params.mets_path} \$mets_file_chunk)
+        \$(${params.env_wrapper_cmd_core} cp -p ${params.mets_path} \$mets_file_chunk)
         """
 }
 
@@ -47,7 +55,7 @@ process ocrd_cis_ocropy_binarize_0 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -69,7 +77,7 @@ process ocrd_anybaseocr_crop_1 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -91,7 +99,7 @@ process ocrd_skimage_binarize_2 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+        ${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
         """
 }
 
@@ -113,7 +121,7 @@ process ocrd_skimage_denoise_3 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -135,7 +143,7 @@ process ocrd_tesserocr_deskew_4 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
         """
 }
 
@@ -157,7 +165,7 @@ process ocrd_cis_ocropy_segment_5 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -179,7 +187,7 @@ process ocrd_cis_ocropy_dewarp_6 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -201,7 +209,7 @@ process ocrd_calamari_recognize_7 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+        ${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
         """
 }
 
@@ -215,8 +223,8 @@ process merging_mets {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
-        ${params.env_wrapper_cmd} rm ${mets_file_chunk}
+        ${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
+        ${params.env_wrapper_cmd_core} rm ${mets_file_chunk}
         """
 }
 
diff --git a/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf b/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
index e864b89a..870ea30c 100644
--- a/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
@@ -7,7 +7,15 @@ params.workspace_dir = "null"
 params.pages = "null"
 params.mets_socket_path = "null"
 params.forks = "4"
-params.env_wrapper_cmd = "null"
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
     debug true
@@ -21,7 +29,7 @@ process split_page_ranges {
 
     script:
         """
-        current_range_pages=\$(${params.env_wrapper_cmd} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
         """
 }
@@ -44,7 +52,7 @@ process ocrd_cis_ocropy_binarize_0 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -66,7 +74,7 @@ process ocrd_anybaseocr_crop_1 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -88,7 +96,7 @@ process ocrd_skimage_binarize_2 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+        ${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
         """
 }
 
@@ -110,7 +118,7 @@ process ocrd_skimage_denoise_3 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -132,7 +140,7 @@ process ocrd_tesserocr_deskew_4 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
         """
 }
 
@@ -154,7 +162,7 @@ process ocrd_cis_ocropy_segment_5 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        ${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
         """
 }
 
@@ -176,7 +184,7 @@ process ocrd_cis_ocropy_dewarp_6 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
         """
 }
 
@@ -198,7 +206,7 @@ process ocrd_calamari_recognize_7 {
 
     script:
         """
-        ${params.env_wrapper_cmd} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+        ${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
         """
 }
 
diff --git a/tests/assets/oton/test_output_nextflow1_local.nf b/tests/assets/oton/test_output_nextflow1_local.nf
index d89109a5..0e2cafde 100644
--- a/tests/assets/oton/test_output_nextflow1_local.nf
+++ b/tests/assets/oton/test_output_nextflow1_local.nf
@@ -6,6 +6,14 @@ params.mets_path = "null"
 params.workspace_dir = "null"
 params.pages = "null"
 params.forks = "4"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
     debug true
diff --git a/tests/assets/oton/test_output_nextflow1_local_with_MS.nf b/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
index 6b9f4eac..8f2655cf 100644
--- a/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
@@ -7,6 +7,14 @@ params.workspace_dir = "null"
 params.pages = "null"
 params.mets_socket_path = "null"
 params.forks = "4"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
     debug true
diff --git a/tests/assets/oton/test_output_nextflow2.nf b/tests/assets/oton/test_output_nextflow2.nf
index 099883e1..43a633f9 100644
--- a/tests/assets/oton/test_output_nextflow2.nf
+++ b/tests/assets/oton/test_output_nextflow2.nf
@@ -6,6 +6,13 @@ params.mets_path = "null"
 params.workspace_dir = "null"
 params.pages = "null"
 params.forks = "4"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
 
 process split_page_ranges {
     debug true
diff --git a/tests/assets/oton/test_output_nextflow3.nf b/tests/assets/oton/test_output_nextflow3.nf
index 205cb236..eaa7ab06 100644
--- a/tests/assets/oton/test_output_nextflow3.nf
+++ b/tests/assets/oton/test_output_nextflow3.nf
@@ -6,6 +6,9 @@ params.mets_path = "null"
 params.workspace_dir = "null"
 params.pages = "null"
 params.forks = "4"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
 
 process split_page_ranges {
     debug true
diff --git a/tests/assets/oton/test_output_nextflow4.nf b/tests/assets/oton/test_output_nextflow4.nf
index a5ef0d12..e1138699 100644
--- a/tests/assets/oton/test_output_nextflow4.nf
+++ b/tests/assets/oton/test_output_nextflow4.nf
@@ -6,6 +6,19 @@ params.mets_path = "null"
 params.workspace_dir = "null"
 params.pages = "null"
 params.forks = "4"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
+params.env_wrapper_cmd_step8 = "null"
+params.env_wrapper_cmd_step9 = "null"
+params.env_wrapper_cmd_step10 = "null"
+params.env_wrapper_cmd_step11 = "null"
+params.env_wrapper_cmd_step12 = "null"
 
 process split_page_ranges {
     debug true
diff --git a/tests/tests_utils/test_2_oton/assert_utils.py b/tests/tests_utils/test_2_oton/assert_utils.py
index 0b2fbbcf..ed197bea 100644
--- a/tests/tests_utils/test_2_oton/assert_utils.py
+++ b/tests/tests_utils/test_2_oton/assert_utils.py
@@ -30,8 +30,8 @@ def assert_common_features_local(nextflow_file_class):
         assert parameter in parameters, f"{parameter} is not in {parameters}"
     blocks_process = nextflow_file_class.nf_blocks_process
     for block in blocks_process:
-        assert '${params.env_wrapper_cmd}' not in block.dump_script(), \
-            "${params.env_wrapper_cmd} found but should not exist in " + f"'{block.ocrd_command_bash_placeholders}'"
+        assert 'params.env_wrapper_cmd_step' not in block.dump_script(), \
+            "params.env_wrapper_cmd_step found but should not exist in " + f"'{block.ocrd_command_bash_placeholders}'"
 
 
 def assert_common_features_docker(nextflow_file_class):
@@ -40,8 +40,8 @@ def assert_common_features_docker(nextflow_file_class):
         assert parameter in parameters, f"{parameter} is not in {parameters}"
     blocks_process = nextflow_file_class.nf_blocks_process
     for block in blocks_process:
-        assert '${params.env_wrapper_cmd}' in block.dump_script(), \
-            "${params.env_wrapper_cmd} not found but should exist in " + f"'{block.ocrd_command_bash_placeholders}'"
+        assert 'params.env_wrapper_cmd_step' in block.dump_script(), \
+            "params.env_wrapper_cmd_step not found but should exist in " + f"'{block.ocrd_command_bash_placeholders}'"
 
 
 def assert_common_features_apptainer(nextflow_file_class):
@@ -50,8 +50,8 @@ def assert_common_features_apptainer(nextflow_file_class):
         assert parameter in parameters, f"{parameter} is not in {parameters}"
     blocks_process = nextflow_file_class.nf_blocks_process
     for block in blocks_process:
-        assert '${params.env_wrapper_cmd}' in block.dump_script(), \
-            "${params.env_wrapper_cmd} not found but should exist in " + f"'{block.ocrd_command_bash_placeholders}'"
+        assert 'params.env_wrapper_cmd_step' in block.dump_script(), \
+            "params.env_wrapper_cmd_step not found but should exist in " + f"'{block.ocrd_command_bash_placeholders}'"
 
 
 def assert_compare_workflow_blocks(output_file_path, expected_wf, clean_files: bool = False):
diff --git a/tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py b/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
similarity index 100%
rename from tests/tests_utils/test_3_hpc/_test_1_nhr_executor.py
rename to tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
diff --git a/tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py b/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
similarity index 100%
rename from tests/tests_utils/test_3_hpc/_test_2_nhr_transfer.py
rename to tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py

From 3762a5f45eaad5a77ea66c93139734c1d16c02fc Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Fri, 29 Nov 2024 13:31:12 +0100
Subject: [PATCH 07/16] fix: oton convert endpoint test

---
 tests/tests_server/test_endpoint_workflow.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/tests_server/test_endpoint_workflow.py b/tests/tests_server/test_endpoint_workflow.py
index 49e68e2f..1b812806 100644
--- a/tests/tests_server/test_endpoint_workflow.py
+++ b/tests/tests_server/test_endpoint_workflow.py
@@ -134,7 +134,7 @@ def test_convert_txt_to_nextflow_success(operandi, auth):
     # Verify the status code and content
     assert_response_status_code(response.status_code, expected_floor=2)
     assert "params.mets_path" in nf_file_content
-    assert "params.env_wrapper" not in nf_file_content
+    assert "params.env_wrapper_cmd_core" not in nf_file_content
     assert "params.mets_socket_path" not in nf_file_content
     assert "merging_mets" in nf_file_content
 
@@ -155,7 +155,7 @@ def test_convert_txt_to_nextflow_success_with_mets_server(operandi, auth):
     # Verify the status code and content
     assert_response_status_code(response.status_code, expected_floor=2)
     assert "params.mets_path" in nf_file_content
-    assert "params.env_wrapper" not in nf_file_content
+    assert "params.env_wrapper_cmd_core" not in nf_file_content
     assert "params.mets_socket_path" in nf_file_content
     assert "merging_mets" not in nf_file_content
 
@@ -207,7 +207,7 @@ def test_convert_txt_to_nextflow_docker_success(operandi, auth):
     nf_file_content = response.content.decode('utf-8')
     assert_response_status_code(response.status_code, expected_floor=2)
     assert "params.mets_path" in nf_file_content
-    assert "params.env_wrapper" in nf_file_content
+    assert "params.env_wrapper_cmd_core" in nf_file_content
     assert "params.mets_socket_path" not in nf_file_content
     assert "merging_mets" in nf_file_content
 
@@ -226,6 +226,6 @@ def test_convert_txt_to_nextflow_docker_success_with_mets_server(operandi, auth)
     nf_file_content = response.content.decode('utf-8')
     assert_response_status_code(response.status_code, expected_floor=2)
     assert "params.mets_path" in nf_file_content
-    assert "params.env_wrapper" in nf_file_content
+    assert "params.env_wrapper_cmd_core" in nf_file_content
     assert "params.mets_socket_path" in nf_file_content
     assert "merging_mets" not in nf_file_content

From f97918074d4c341762203401a5b1775c25a7ce11 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Fri, 29 Nov 2024 13:53:48 +0100
Subject: [PATCH 08/16] fix: checking whether a nf script uses mets server

---
 src/server/operandi_server/routers/workflow_utils.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/server/operandi_server/routers/workflow_utils.py b/src/server/operandi_server/routers/workflow_utils.py
index 94c2e6e2..49d2a517 100644
--- a/src/server/operandi_server/routers/workflow_utils.py
+++ b/src/server/operandi_server/routers/workflow_utils.py
@@ -1,9 +1,11 @@
 from fastapi import HTTPException, status
 from pathlib import Path
+from typing import List
 
 from operandi_utils.database import db_get_workflow, db_get_workflow_job
 from operandi_utils.database.models import DBWorkflow, DBWorkflowJob
 from operandi_utils.oton import OTONConverter, OCRDValidator
+from operandi_utils.oton.constants import PARAMS_KEY_METS_SOCKET_PATH
 
 
 async def get_db_workflow_with_handling(
@@ -41,7 +43,7 @@ async def get_db_workflow_job_with_handling(logger, job_id: str, check_local_exi
 
 
 async def nf_script_uses_mets_server_with_handling(
-    logger, nf_script_path: str, search_string: str = "params.mets_socket"
+    logger, nf_script_path: str, search_string: str = PARAMS_KEY_METS_SOCKET_PATH
 ) -> bool:
     try:
         with open(nf_script_path) as nf_file:

From c66fcdef92bd196de4c83cbb67fe4fed3ec4f5c1 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Fri, 29 Nov 2024 16:54:42 +0100
Subject: [PATCH 09/16] another big portion of working changes

---
 src/broker/operandi_broker/worker.py          |  14 +-
 .../operandi_server/routers/workflow.py       |  48 +++-
 .../operandi_server/routers/workflow_utils.py |  28 +-
 src/server/operandi_server/server.py          |   1 +
 src/utils/operandi_utils/__init__.py          |   6 +-
 src/utils/operandi_utils/constants.py         |   3 +-
 .../operandi_utils/database/db_workflow.py    |  12 +-
 src/utils/operandi_utils/database/models.py   |   2 +
 .../nextflow_workflows/default_workflow.nf    | 222 ++++++++--------
 .../default_workflow_with_MS.nf               | 192 ++++++++------
 .../hpc/nextflow_workflows/odem_workflow.nf   | 240 ++++++++++--------
 .../odem_workflow_with_MS.nf                  | 208 +++++++++------
 .../hpc/nextflow_workflows/sbb_workflow.nf    |  83 +++---
 .../sbb_workflow_with_MS.nf                   |  69 +++--
 .../nextflow_workflows/template_workflow.nf   |  83 +++---
 .../template_workflow_with_MS.nf              |  69 +++--
 src/utils/operandi_utils/hpc/nhr_executor.py  |  27 +-
 .../default_workflow.txt                      |   9 +
 .../ocrd_process_workflows/odem_workflow.txt  |  11 +
 .../ocrd_process_workflows/sbb_workflow.txt   |   2 +
 .../template_workflow.txt                     |   2 +
 .../operandi_utils/oton/nf_block_workflow.py  |   2 +-
 .../operandi_utils/oton/nf_file_executable.py |   6 +-
 src/utils/operandi_utils/utils.py             |   4 +-
 tests/assets/oton/constants.py                |  10 +-
 .../oton/test_output_nextflow1_apptainer.nf   |   2 +-
 ...test_output_nextflow1_apptainer_with_MS.nf |   4 +-
 .../oton/test_output_nextflow1_docker.nf      |   2 +-
 .../test_output_nextflow1_docker_with_MS.nf   |   4 +-
 .../oton/test_output_nextflow1_local.nf       |   2 +-
 .../test_output_nextflow1_local_with_MS.nf    |   4 +-
 tests/assets/oton/test_output_nextflow2.nf    |   2 +-
 tests/assets/oton/test_output_nextflow3.nf    |   2 +-
 tests/assets/oton/test_output_nextflow4.nf    |   2 +-
 tests/tests_server/test_endpoint_workflow.py  |  17 +-
 .../test_3_hpc/test_1_nhr_executor.py         |   8 +-
 .../test_3_hpc/test_2_nhr_transfer.py         |   4 +-
 .../test_3_hpc/test_3_nhr_combined.py         |   8 +-
 38 files changed, 816 insertions(+), 598 deletions(-)
 create mode 100644 src/utils/operandi_utils/hpc/ocrd_process_workflows/default_workflow.txt
 create mode 100644 src/utils/operandi_utils/hpc/ocrd_process_workflows/odem_workflow.txt
 create mode 100644 src/utils/operandi_utils/hpc/ocrd_process_workflows/sbb_workflow.txt
 create mode 100644 src/utils/operandi_utils/hpc/ocrd_process_workflows/template_workflow.txt

diff --git a/src/broker/operandi_broker/worker.py b/src/broker/operandi_broker/worker.py
index 181614ea..5c709628 100644
--- a/src/broker/operandi_broker/worker.py
+++ b/src/broker/operandi_broker/worker.py
@@ -5,6 +5,7 @@
 from os.path import join
 from pathlib import Path
 from sys import exit
+from typing import List
 
 from operandi_utils import reconfigure_all_loggers, get_log_file_path_prefix
 from operandi_utils.constants import LOG_LEVEL_WORKER, StateJob, StateWorkspace
@@ -111,6 +112,7 @@ def __callback(self, ch, method, properties, body):
 
             workflow_script_path = Path(workflow_db.workflow_script_path)
             nf_uses_mets_server = workflow_db.uses_mets_server
+            nf_executable_steps = workflow_db.executable_steps
             workspace_dir = Path(workspace_db.workspace_dir)
             mets_basename = workspace_db.mets_basename
             ws_pages_amount = workspace_db.pages_amount
@@ -132,8 +134,8 @@ def __callback(self, ch, method, properties, body):
                 workspace_dir=workspace_dir, workspace_base_mets=mets_basename,
                 workflow_script_path=workflow_script_path, input_file_grp=input_file_grp,
                 nf_process_forks=nf_process_forks, ws_pages_amount=ws_pages_amount, use_mets_server=nf_uses_mets_server,
-                file_groups_to_remove=remove_file_grps, cpus=slurm_job_cpus, ram=slurm_job_ram,
-                partition=slurm_job_partition
+                nf_executable_steps=nf_executable_steps, file_groups_to_remove=remove_file_grps, cpus=slurm_job_cpus,
+                ram=slurm_job_ram, partition=slurm_job_partition
             )
             self.log.info(f"The HPC slurm job was successfully submitted")
         except Exception as error:
@@ -200,7 +202,8 @@ def signal_handler(self, sig, frame):
     def prepare_and_trigger_slurm_job(
         self, workflow_job_id: str, workspace_id: str, workspace_dir: Path, workspace_base_mets: str,
         workflow_script_path: Path, input_file_grp: str, nf_process_forks: int, ws_pages_amount: int,
-        use_mets_server: bool, file_groups_to_remove: str, cpus: int, ram: int, partition: str
+        use_mets_server: bool, nf_executable_steps: List[str], file_groups_to_remove: str, cpus: int, ram: int,
+        partition: str
     ) -> str:
         if self.test_sbatch:
             job_deadline_time = HPC_JOB_DEADLINE_TIME_TEST
@@ -232,8 +235,9 @@ def prepare_and_trigger_slurm_job(
                 workflow_job_id=workflow_job_id, nextflow_script_path=workflow_script_path,
                 workspace_id=workspace_id, mets_basename=workspace_base_mets,
                 input_file_grp=input_file_grp, nf_process_forks=nf_process_forks, ws_pages_amount=ws_pages_amount,
-                use_mets_server=use_mets_server, file_groups_to_remove=file_groups_to_remove, cpus=cpus, ram=ram,
-                job_deadline_time=job_deadline_time, partition=partition, qos=qos)
+                use_mets_server=use_mets_server, nf_executable_steps=nf_executable_steps,
+                file_groups_to_remove=file_groups_to_remove, cpus=cpus, ram=ram, job_deadline_time=job_deadline_time,
+                partition=partition, qos=qos)
         except Exception as error:
             db_stats = sync_db_increase_processing_stats(
                 find_user_id=self.current_message_user_id, pages_failed=ws_pages_amount)
diff --git a/src/server/operandi_server/routers/workflow.py b/src/server/operandi_server/routers/workflow.py
index ab26bf00..5a7a1121 100644
--- a/src/server/operandi_server/routers/workflow.py
+++ b/src/server/operandi_server/routers/workflow.py
@@ -12,11 +12,12 @@
 from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from starlette.status import HTTP_404_NOT_FOUND
 
-from operandi_utils import get_nf_workflows_dir
+from operandi_utils import get_nf_wfs_dir, get_ocrd_process_wfs_dir
 from operandi_utils.constants import AccountType, ServerApiTag, StateJob, StateWorkspace
 from operandi_utils.database import (
     db_create_workflow, db_create_workflow_job, db_get_hpc_slurm_job, db_get_workflow, db_update_workspace,
     db_increase_processing_stats_with_handling)
+from operandi_utils.oton import OTONConverter
 from operandi_utils.rabbitmq import (
     get_connection_publisher, RABBITMQ_QUEUE_JOB_STATUSES, RABBITMQ_QUEUE_HARVESTER, RABBITMQ_QUEUE_USERS)
 from operandi_server.constants import (
@@ -30,7 +31,7 @@
     get_db_workflow_job_with_handling,
     get_db_workflow_with_handling,
     nf_script_uses_mets_server_with_handling,
-    validate_oton_with_handling
+    validate_oton_with_handling, nf_script_executable_steps_with_handling
 )
 from .workspace_utils import check_if_file_group_exists_with_handling, get_db_workspace_with_handling
 from .user import RouterUser
@@ -133,10 +134,32 @@ async def _push_status_request_to_rabbitmq(self, job_id: str):
             self.logger.error(f"{message}, error: {error}")
             raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=message)
 
-    async def insert_production_workflows(self, production_workflows_dir: Path = get_nf_workflows_dir()):
+    async def produce_production_workflows(
+        self,
+        ocrd_process_wf_dir: Path = get_ocrd_process_wfs_dir(),
+        production_nf_wfs_dir: Path = get_nf_wfs_dir()
+    ):
+        oton_converter = OTONConverter()
+        for path in ocrd_process_wf_dir.iterdir():
+            if not path.is_file():
+                self.logger.info(f"Skipping non-file path: {path}")
+                continue
+            if path.suffix != '.txt':
+                self.logger.info(f"Skipping non .txt extension file path: {path}")
+                continue
+            # path.stem -> file_name
+            # path.name -> file_name.ext
+            output_path = Path(production_nf_wfs_dir, f"{path.stem}.nf")
+            oton_converter.convert_oton(
+                input_path=path, output_path=str(output_path), environment="apptainer", with_mets_server=False)
+            output_path = Path(production_nf_wfs_dir, f"{path.stem}_with_MS.nf")
+            oton_converter.convert_oton(
+                input_path=path, output_path=str(output_path), environment="apptainer", with_mets_server=True)
+
+    async def insert_production_workflows(self, production_nf_wfs_dir: Path = get_nf_wfs_dir()):
         wf_detail = "Workflow provided by the Operandi Server"
-        self.logger.info(f"Inserting production workflows for Operandi from: {production_workflows_dir}")
-        for path in production_workflows_dir.iterdir():
+        self.logger.info(f"Inserting production workflows for Operandi from: {production_nf_wfs_dir}")
+        for path in production_nf_wfs_dir.iterdir():
             if not path.is_file():
                 self.logger.info(f"Skipping non-file path: {path}")
                 continue
@@ -150,11 +173,14 @@ async def insert_production_workflows(self, production_workflows_dir: Path = get
             nf_script_dest = join(workflow_dir, path.name)
             copyfile(src=path, dst=nf_script_dest)
             uses_mets_server = await nf_script_uses_mets_server_with_handling(self.logger, nf_script_dest)
-            self.logger.info(f"Inserting: {workflow_id}, uses_mets_server: {uses_mets_server}, script path: {nf_script_dest}")
+            executable_steps = await nf_script_executable_steps_with_handling(self.logger, nf_script_dest)
+            self.logger.info(
+                f"Inserting: {workflow_id}, uses_mets_server: {uses_mets_server}, script path: {nf_script_dest}")
             await db_create_workflow(
                 user_id="Operandi Server",
                 workflow_id=workflow_id, workflow_dir=workflow_dir, workflow_script_path=nf_script_dest,
-                workflow_script_base=path.name, uses_mets_server=uses_mets_server, details=wf_detail)
+                workflow_script_base=path.name, uses_mets_server=uses_mets_server, executable_steps=executable_steps,
+                details=wf_detail)
             self.production_workflows.append(workflow_id)
 
     async def list_workflows(self, auth: HTTPBasicCredentials = Depends(HTTPBasic())) -> List[WorkflowRsrc]:
@@ -204,10 +230,11 @@ async def upload_workflow_script(
             self.logger.error(f"{message}, error: {error}")
             raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)
         uses_mets_server = await nf_script_uses_mets_server_with_handling(self.logger, nf_script_dest)
+        executable_steps = await nf_script_executable_steps_with_handling(self.logger, nf_script_dest)
         db_workflow = await db_create_workflow(
             user_id=py_user_action.user_id, workflow_id=workflow_id, workflow_dir=workflow_dir,
             workflow_script_path=nf_script_dest, workflow_script_base=nextflow_script.filename,
-            uses_mets_server=uses_mets_server, details=details)
+            uses_mets_server=uses_mets_server, executable_steps=executable_steps, details=details)
         return WorkflowRsrc.from_db_workflow(db_workflow)
 
     async def update_workflow_script(
@@ -239,10 +266,11 @@ async def update_workflow_script(
             self.logger.error(f"{message}, error: {error}")
             raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=message)
         uses_mets_server = await nf_script_uses_mets_server_with_handling(self.logger, nf_script_dest)
+        executable_steps = await nf_script_executable_steps_with_handling(self.logger, nf_script_dest)
         db_workflow = await db_create_workflow(
             user_id=py_user_action.user_id, workflow_id=workflow_id, workflow_dir=workflow_dir,
             workflow_script_path=nf_script_dest, workflow_script_base=nextflow_script.filename,
-            uses_mets_server=uses_mets_server, details=details)
+            uses_mets_server=uses_mets_server, executable_steps=executable_steps, details=details)
         return WorkflowRsrc.from_db_workflow(db_workflow)
 
     async def get_workflow_job_status(
@@ -461,4 +489,4 @@ async def convert_txt_to_nextflow(
 
         await validate_oton_with_handling(self.logger, ocrd_process_txt)
         await convert_oton_with_handling(self.logger, ocrd_process_txt, nf_script_dest, environment, with_mets_server)
-        return FileResponse(nf_script_dest, filename=f'{oton_id}.nf')
+        return FileResponse(nf_script_dest, filename=f'{oton_id}.nf', media_type="application/txt-file")
diff --git a/src/server/operandi_server/routers/workflow_utils.py b/src/server/operandi_server/routers/workflow_utils.py
index 49d2a517..39a837fa 100644
--- a/src/server/operandi_server/routers/workflow_utils.py
+++ b/src/server/operandi_server/routers/workflow_utils.py
@@ -41,7 +41,6 @@ async def get_db_workflow_job_with_handling(logger, job_id: str, check_local_exi
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=message)
     return db_workflow_job
 
-
 async def nf_script_uses_mets_server_with_handling(
     logger, nf_script_path: str, search_string: str = PARAMS_KEY_METS_SOCKET_PATH
 ) -> bool:
@@ -58,6 +57,33 @@ async def nf_script_uses_mets_server_with_handling(
         logger.error(f"{message}, error: {error}")
         raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=message)
 
+async def nf_script_executable_steps_with_handling(logger, nf_script_path: str) -> List[str]:
+    processor_executables: List[str] = []
+    try:
+        with open(nf_script_path) as nf_file:
+            line = nf_file.readline()
+            for word in line.split(' '):
+                if "ocrd-" in word:
+                    processor_executables.append(word)
+                    break
+    except Exception as error:
+        message = "Failed to identify processor executables in the provided Nextflow workflow."
+        logger.error(f"{message}, error: {error}")
+        raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=message)
+
+    """
+    apptainer_images: List[str] = []
+    try:
+        for executable in processor_executables:
+            apptainer_images.append(OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE[executable])
+    except Exception as error:
+        message = "Failed to produce apptainer image names from the processor executables list"
+        logger.error(f"{message}, error: {error}")
+        raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=message)
+    return apptainer_images
+    """
+
+    return processor_executables
 
 async def validate_oton_with_handling(logger, ocrd_process_txt_path: str):
     try:
diff --git a/src/server/operandi_server/server.py b/src/server/operandi_server/server.py
index c413cf2f..6c8eb873 100644
--- a/src/server/operandi_server/server.py
+++ b/src/server/operandi_server/server.py
@@ -114,6 +114,7 @@ async def include_webapi_routers(self):
         self.include_router(RouterDiscovery().router)
         self.include_router(RouterUser().router)
         workflow_router = RouterWorkflow()
+        await workflow_router.produce_production_workflows()
         await workflow_router.insert_production_workflows()
         self.include_router(workflow_router.router)
         self.include_router(RouterWorkspace().router)
diff --git a/src/utils/operandi_utils/__init__.py b/src/utils/operandi_utils/__init__.py
index 6cbc04c8..0fd74c2f 100644
--- a/src/utils/operandi_utils/__init__.py
+++ b/src/utils/operandi_utils/__init__.py
@@ -4,7 +4,8 @@
     "is_url_responsive",
     "generate_id",
     "get_log_file_path_prefix",
-    "get_nf_workflows_dir",
+    "get_nf_wfs_dir",
+    "get_ocrd_process_wfs_dir",
     "make_zip_archive",
     "receive_file",
     "reconfigure_all_loggers",
@@ -25,7 +26,8 @@
     download_mets_file,
     is_url_responsive,
     generate_id,
-    get_nf_workflows_dir,
+    get_nf_wfs_dir,
+    get_ocrd_process_wfs_dir,
     receive_file,
     make_zip_archive,
     unpack_zip_archive,
diff --git a/src/utils/operandi_utils/constants.py b/src/utils/operandi_utils/constants.py
index 57fe6e17..c38f33cb 100644
--- a/src/utils/operandi_utils/constants.py
+++ b/src/utils/operandi_utils/constants.py
@@ -18,6 +18,7 @@
     "LOG_LEVEL_SERVER",
     "LOG_LEVEL_WORKER",
     "MODULE_TYPES",
+    "OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE",
     "OLA_HD_BAG_ENDPOINT",
     "OLA_HD_USER",
     "OLA_HD_PASSWORD",
@@ -167,7 +168,7 @@ class StateWorkspace(str, Enum):
     UNSET = "UNSET"
 
 # TODO: Find a more optimal way of achieving this dynamically
-OCRD_PROCESSOR_NAME_TO_IMAGE = {
+OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE = {
     "ocrd": "ocrd_core.sif",
     "ocrd-tesserocr-crop": "ocrd_tesserocr.sif",
     "ocrd-tesserocr-deskew": "ocrd_tesserocr.sif",
diff --git a/src/utils/operandi_utils/database/db_workflow.py b/src/utils/operandi_utils/database/db_workflow.py
index 03e0d074..b012c16f 100644
--- a/src/utils/operandi_utils/database/db_workflow.py
+++ b/src/utils/operandi_utils/database/db_workflow.py
@@ -1,4 +1,5 @@
 from datetime import datetime
+from typing import List
 from operandi_utils import call_sync
 from .models import DBWorkflow
 
@@ -6,7 +7,7 @@
 # TODO: This also updates to satisfy the PUT method in the Workflow Manager - fix this
 async def db_create_workflow(
     user_id: str, workflow_id: str, workflow_dir: str, workflow_script_base: str, workflow_script_path: str,
-    uses_mets_server: bool, details: str = "Workflow"
+    uses_mets_server: bool, executable_steps: List[str], details: str = "Workflow"
 ) -> DBWorkflow:
     try:
         db_workflow = await db_get_workflow(workflow_id)
@@ -18,6 +19,7 @@ async def db_create_workflow(
             workflow_script_base=workflow_script_base,
             workflow_script_path=workflow_script_path,
             uses_mets_server=uses_mets_server,
+            executable_steps=executable_steps,
             datetime=datetime.now(),
             details=details
         )
@@ -28,6 +30,7 @@ async def db_create_workflow(
         db_workflow.workflow_script_base = workflow_script_base
         db_workflow.workflow_script_path = workflow_script_path
         db_workflow.uses_mets_server = uses_mets_server
+        db_workflow.executable_steps = executable_steps
         db_workflow.details = details
     await db_workflow.save()
     return db_workflow
@@ -36,10 +39,11 @@ async def db_create_workflow(
 @call_sync
 async def sync_db_create_workflow(
     user_id: str, workflow_id: str, workflow_dir: str, workflow_script_base: str, workflow_script_path: str,
-    uses_mets_server: bool, details: str = "Workflow"
+    uses_mets_server: bool, executable_steps: List[str], details: str = "Workflow"
 ) -> DBWorkflow:
     return await db_create_workflow(
-        user_id, workflow_id, workflow_dir, workflow_script_base, workflow_script_path, uses_mets_server, details)
+        user_id, workflow_id, workflow_dir, workflow_script_base, workflow_script_path, uses_mets_server,
+        executable_steps, details)
 
 
 async def db_get_workflow(workflow_id: str) -> DBWorkflow:
@@ -70,6 +74,8 @@ async def db_update_workflow(find_workflow_id: str, **kwargs) -> DBWorkflow:
             db_workflow.workflow_script_path = value
         elif key == "uses_mets_server":
             db_workflow.uses_mets_server = value
+        elif key == "executable_steps":
+            db_workflow.executable_steps = value
         elif key == "deleted":
             db_workflow.deleted = value
         elif key == "details":
diff --git a/src/utils/operandi_utils/database/models.py b/src/utils/operandi_utils/database/models.py
index d587e589..d885df0e 100644
--- a/src/utils/operandi_utils/database/models.py
+++ b/src/utils/operandi_utils/database/models.py
@@ -102,6 +102,7 @@ class DBWorkflow(Document):
         workflow_script_base    The name of the nextflow script file
         workflow_script_path    Nextflow workflow file full path on the server
         uses_mets_server        Whether the NF script forwards requests to a workspace mets server
+        executable_steps        A list of ocrd_processor executables
         deleted                 Whether the entry has been deleted locally from the server
         datetime                Shows the created date time of the entry
         details                 Extra user specified details about this entry
@@ -112,6 +113,7 @@ class DBWorkflow(Document):
     workflow_script_base: str
     workflow_script_path: str
     uses_mets_server: bool
+    executable_steps: List[str]
     deleted: bool = False
     datetime = datetime.now()
     details: Optional[str]
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
index ca8b2a11..b057341e 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
@@ -1,250 +1,268 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - Default Workflow
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
         env mets_file_chunk
         env current_range_pages
+
     script:
-    """
-    current_range_pages=\$(${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
-    echo "Current range is: \$current_range_pages"
-    mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
-    echo "Mets file chunk path: \$mets_file_chunk"
-    \$(${params.singularity_wrapper} cp -p ${params.mets} \$mets_file_chunk)
-    """
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
+        echo "Mets file chunk path: \$mets_file_chunk"
+        \$(${params.env_wrapper_cmd_core} cp -p ${params.mets_path} \$mets_file_chunk)
+        """
 }
 
-process ocrd_cis_ocropy_binarize {
+process ocrd_cis_ocropy_binarize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-binarize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
-process ocrd_anybaseocr_crop {
+process ocrd_anybaseocr_crop_1 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-anybaseocr-crop -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
-process ocrd_skimage_binarize {
+process ocrd_skimage_binarize_2 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-skimage-binarize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P method "li"
-    """
+        """
+        ${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+        """
 }
 
-process ocrd_skimage_denoise {
+process ocrd_skimage_denoise_3 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-skimage-denoise -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
-    """
+        """
+        ${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        """
 }
 
-process ocrd_tesserocr_deskew {
+process ocrd_tesserocr_deskew_4 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-deskew -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P operation_level "page"
-    """
+        """
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+        """
 }
 
-process ocrd_cis_ocropy_segment {
+process ocrd_cis_ocropy_segment_5 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
-    """
+        """
+        ${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        """
 }
 
-process ocrd_cis_ocropy_dewarp {
+process ocrd_cis_ocropy_dewarp_6 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-dewarp -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
-process ocrd_calamari_recognize {
+process ocrd_calamari_recognize_7 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-calamari-recognize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P checkpoint_dir "qurator-gt4histocr-1.0"
-    """
+        """
+        ${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+        """
 }
 
 process merging_mets {
-    // Must be a single instance - modifying the main mets file
+    debug true
     maxForks 1
+    cpus params.cpus_per_fork
+    memory params.ram_per_fork
 
     input:
         val mets_file_chunk
         val page_range
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
-    ${params.singularity_wrapper} rm ${mets_file_chunk}
-    """
+        """
+        ${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
+        ${params.env_wrapper_cmd_core} rm ${mets_file_chunk}
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize(split_page_ranges.out[0], split_page_ranges.out[1], params.input_file_group, "OCR-D-BIN")
-        ocrd_anybaseocr_crop(ocrd_cis_ocropy_binarize.out[0], ocrd_cis_ocropy_binarize.out[1], "OCR-D-BIN", "OCR-D-CROP")
-        ocrd_skimage_binarize(ocrd_anybaseocr_crop.out[0], ocrd_anybaseocr_crop.out[1], "OCR-D-CROP", "OCR-D-BIN2")
-        ocrd_skimage_denoise(ocrd_skimage_binarize.out[0], ocrd_skimage_binarize.out[1], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
-        ocrd_tesserocr_deskew(ocrd_skimage_denoise.out[0], ocrd_skimage_denoise.out[1], "OCR-D-BIN-DENOISE", "OCR-D-BIN-DENOISE-DESKEW")
-        ocrd_cis_ocropy_segment(ocrd_tesserocr_deskew.out[0], ocrd_tesserocr_deskew.out[1], "OCR-D-BIN-DENOISE-DESKEW", "OCR-D-SEG")
-        ocrd_cis_ocropy_dewarp(ocrd_cis_ocropy_segment.out[0], ocrd_cis_ocropy_segment.out[1], "OCR-D-SEG", "OCR-D-SEG-LINE-RESEG-DEWARP")
-        ocrd_calamari_recognize(ocrd_cis_ocropy_dewarp.out[0], ocrd_cis_ocropy_dewarp.out[1], "OCR-D-SEG-LINE-RESEG-DEWARP", "OCR-D-OCR")
-        merging_mets(ocrd_calamari_recognize.out[0], ocrd_calamari_recognize.out[1])
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
+        ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
+        ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
+        ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
+        ocrd_tesserocr_deskew_4(ocrd_skimage_denoise_3.out[0], ocrd_skimage_denoise_3.out[1], ocrd_skimage_denoise_3.out[2], "OCR-D-BIN-DENOISE", "OCR-D-BIN-DENOISE-DESKEW")
+        ocrd_cis_ocropy_segment_5(ocrd_tesserocr_deskew_4.out[0], ocrd_tesserocr_deskew_4.out[1], ocrd_tesserocr_deskew_4.out[2], "OCR-D-BIN-DENOISE-DESKEW", "OCR-D-SEG")
+        ocrd_cis_ocropy_dewarp_6(ocrd_cis_ocropy_segment_5.out[0], ocrd_cis_ocropy_segment_5.out[1], ocrd_cis_ocropy_segment_5.out[2], "OCR-D-SEG", "OCR-D-SEG-LINE-RESEG-DEWARP")
+        ocrd_calamari_recognize_7(ocrd_cis_ocropy_dewarp_6.out[0], ocrd_cis_ocropy_dewarp_6.out[1], ocrd_cis_ocropy_dewarp_6.out[2], "OCR-D-SEG-LINE-RESEG-DEWARP", "OCR-D-OCR")
+        merging_mets(ocrd_calamari_recognize_7.out[0], ocrd_calamari_recognize_7.out[1])
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
index 8833a502..590ba3c4 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
@@ -1,217 +1,249 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
-params.mets_socket = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
+params.mets_socket_path = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - Default Workflow with Mets Server
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    mets_socket         : ${params.mets_socket}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
+        env mets_file_chunk
         env current_range_pages
-    shell:
-    '''
-    current_range_pages=$(!{params.singularity_wrapper} ocrd workspace -d !{params.workspace_dir} list-page -f comma-separated -D !{params.forks} -C !{range_multiplier})
-    echo "Current range is: $current_range_pages"
-    '''
+
+    script:
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
+        """
 }
 
-process ocrd_cis_ocropy_binarize {
+process ocrd_cis_ocropy_binarize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-binarize -U ${params.mets_socket} -w ${params.workspace_dir} --page-id ${page_range} -m ${params.mets} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
-process ocrd_anybaseocr_crop {
+process ocrd_anybaseocr_crop_1 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-anybaseocr-crop -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
-process ocrd_skimage_binarize {
+process ocrd_skimage_binarize_2 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-skimage-binarize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P method "li"
-    """
+        """
+        ${params.env_wrapper_cmd_step2} ocrd-skimage-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+        """
 }
 
-process ocrd_skimage_denoise {
+process ocrd_skimage_denoise_3 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-skimage-denoise -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
-    """
+        """
+        ${params.env_wrapper_cmd_step3} ocrd-skimage-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        """
 }
 
-process ocrd_tesserocr_deskew {
+process ocrd_tesserocr_deskew_4 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-deskew -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P operation_level "page"
-    """
+        """
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+        """
 }
 
-process ocrd_cis_ocropy_segment {
+process ocrd_cis_ocropy_segment_5 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
-    """
+        """
+        ${params.env_wrapper_cmd_step5} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        """
 }
 
-process ocrd_cis_ocropy_dewarp {
+process ocrd_cis_ocropy_dewarp_6 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-dewarp -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
-process ocrd_calamari_recognize {
+process ocrd_calamari_recognize_7 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-calamari-recognize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P checkpoint_dir "qurator-gt4histocr-1.0"
-    """
+        """
+        ${params.env_wrapper_cmd_step7} ocrd-calamari-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize(split_page_ranges.out, params.input_file_group, "OCR-D-BIN")
-        ocrd_anybaseocr_crop(ocrd_cis_ocropy_binarize.out, "OCR-D-BIN", "OCR-D-CROP")
-        ocrd_skimage_binarize(ocrd_anybaseocr_crop.out, "OCR-D-CROP", "OCR-D-BIN2")
-        ocrd_skimage_denoise(ocrd_skimage_binarize.out, "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
-        ocrd_tesserocr_deskew(ocrd_skimage_denoise.out, "OCR-D-BIN-DENOISE", "OCR-D-BIN-DENOISE-DESKEW")
-        ocrd_cis_ocropy_segment(ocrd_tesserocr_deskew.out, "OCR-D-BIN-DENOISE-DESKEW", "OCR-D-SEG")
-        ocrd_cis_ocropy_dewarp(ocrd_cis_ocropy_segment.out, "OCR-D-SEG", "OCR-D-SEG-LINE-RESEG-DEWARP")
-        ocrd_calamari_recognize(ocrd_cis_ocropy_dewarp.out, "OCR-D-SEG-LINE-RESEG-DEWARP", "OCR-D-OCR")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
+        ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
+        ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
+        ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
+        ocrd_tesserocr_deskew_4(ocrd_skimage_denoise_3.out[0], ocrd_skimage_denoise_3.out[1], ocrd_skimage_denoise_3.out[2], "OCR-D-BIN-DENOISE", "OCR-D-BIN-DENOISE-DESKEW")
+        ocrd_cis_ocropy_segment_5(ocrd_tesserocr_deskew_4.out[0], ocrd_tesserocr_deskew_4.out[1], ocrd_tesserocr_deskew_4.out[2], "OCR-D-BIN-DENOISE-DESKEW", "OCR-D-SEG")
+        ocrd_cis_ocropy_dewarp_6(ocrd_cis_ocropy_segment_5.out[0], ocrd_cis_ocropy_segment_5.out[1], ocrd_cis_ocropy_segment_5.out[2], "OCR-D-SEG", "OCR-D-SEG-LINE-RESEG-DEWARP")
+        ocrd_calamari_recognize_7(ocrd_cis_ocropy_dewarp_6.out[0], ocrd_cis_ocropy_dewarp_6.out[1], ocrd_cis_ocropy_dewarp_6.out[2], "OCR-D-SEG-LINE-RESEG-DEWARP", "OCR-D-OCR")
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
index 57dd0b48..78c6f2c2 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
@@ -1,294 +1,320 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - Odem Workflow
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
+params.env_wrapper_cmd_step8 = "null"
+params.env_wrapper_cmd_step9 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
         env mets_file_chunk
         env current_range_pages
+
     script:
-    """
-    current_range_pages=\$(${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
-    echo "Current range is: \$current_range_pages"
-    mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
-    echo "Mets file chunk path: \$mets_file_chunk"
-    \$(${params.singularity_wrapper} cp -p ${params.mets} \$mets_file_chunk)
-    """
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
+        echo "Mets file chunk path: \$mets_file_chunk"
+        \$(${params.env_wrapper_cmd_core} cp -p ${params.mets_path} \$mets_file_chunk)
+        """
 }
 
 process ocrd_cis_ocropy_binarize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-binarize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_anybaseocr_crop_1 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-anybaseocr-crop -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_cis_ocropy_denoise_2 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-denoise -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step2} ocrd-cis-ocropy-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_cis_ocropy_deskew_3 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-deskew -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation page
-    """
+        """
+        ${params.env_wrapper_cmd_step3} ocrd-cis-ocropy-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        """
 }
 
 process ocrd_tesserocr_segment_region_4 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-segment-region -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P padding 5.0 -P find_tables false -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-segment-region -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"padding": 5.0, "find_tables": false, "dpi": 300}'
+        """
 }
 
 process ocrd_segment_repair_5 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-segment-repair -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P plausibilize true -P plausibilize_merge_min_overlap 0.7
-    """
+        """
+        ${params.env_wrapper_cmd_step5} ocrd-segment-repair -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"plausibilize": true, "plausibilize_merge_min_overlap": 0.7}'
+        """
 }
 
 process ocrd_cis_ocropy_clip_6 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-clip -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-clip -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
 process ocrd_cis_ocropy_segment_7 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step7} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_cis_ocropy_dewarp_8 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-dewarp -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step8} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
 process ocrd_tesserocr_recognize_9 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-recognize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P model Fraktur
-    """
+        """
+        ${params.env_wrapper_cmd_step9} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"model": "Fraktur"}'
+        """
 }
 
 process merging_mets {
-    // Must be a single instance - modifying the main mets file
+    debug true
     maxForks 1
+    cpus params.cpus_per_fork
+    memory params.ram_per_fork
 
     input:
         val mets_file_chunk
         val page_range
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
-    ${params.singularity_wrapper} rm ${mets_file_chunk}
-    """
+        """
+        ${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
+        ${params.env_wrapper_cmd_core} rm ${mets_file_chunk}
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.input_file_group, "OCR-D-BINPAGE")
-        ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], "OCR-D-BINPAGE", "OCR-D-SEG-PAGE-ANYOCR")
-        ocrd_cis_ocropy_denoise_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], "OCR-D-SEG-PAGE-ANYOCR", "OCR-D-DENOISE-OCROPY")
-        ocrd_cis_ocropy_deskew_3(ocrd_cis_ocropy_denoise_2.out[0], ocrd_cis_ocropy_denoise_2.out[1], "OCR-D-DENOISE-OCROPY", "OCR-D-DESKEW-OCROPY")
-        ocrd_tesserocr_segment_region_4(ocrd_cis_ocropy_deskew_3.out[0], ocrd_cis_ocropy_deskew_3.out[1], "OCR-D-DESKEW-OCROPY", "OCR-D-SEG-BLOCK-TESSERACT")
-        ocrd_segment_repair_5(ocrd_tesserocr_segment_region_4.out[0], ocrd_tesserocr_segment_region_4.out[1], "OCR-D-SEG-BLOCK-TESSERACT", "OCR-D-SEGMENT-REPAIR")
-        ocrd_cis_ocropy_clip_6(ocrd_segment_repair_5.out[0], ocrd_segment_repair_5.out[1], "OCR-D-SEGMENT-REPAIR", "OCR-D-CLIP")
-        ocrd_cis_ocropy_segment_7(ocrd_cis_ocropy_clip_6.out[0], ocrd_cis_ocropy_clip_6.out[1], "OCR-D-CLIP", "OCR-D-SEGMENT-OCROPY")
-        ocrd_cis_ocropy_dewarp_8(ocrd_cis_ocropy_segment_7.out[0], ocrd_cis_ocropy_segment_7.out[1], "OCR-D-SEGMENT-OCROPY", "OCR-D-DEWARP")
-        ocrd_tesserocr_recognize_9(ocrd_cis_ocropy_dewarp_8.out[0], ocrd_cis_ocropy_dewarp_8.out[1], "OCR-D-DEWARP", "OCR-D-OCR")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BINPAGE")
+        ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BINPAGE", "OCR-D-SEG-PAGE-ANYOCR")
+        ocrd_cis_ocropy_denoise_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-SEG-PAGE-ANYOCR", "OCR-D-DENOISE-OCROPY")
+        ocrd_cis_ocropy_deskew_3(ocrd_cis_ocropy_denoise_2.out[0], ocrd_cis_ocropy_denoise_2.out[1], ocrd_cis_ocropy_denoise_2.out[2], "OCR-D-DENOISE-OCROPY", "OCR-D-DESKEW-OCROPY")
+        ocrd_tesserocr_segment_region_4(ocrd_cis_ocropy_deskew_3.out[0], ocrd_cis_ocropy_deskew_3.out[1], ocrd_cis_ocropy_deskew_3.out[2], "OCR-D-DESKEW-OCROPY", "OCR-D-SEG-BLOCK-TESSERACT")
+        ocrd_segment_repair_5(ocrd_tesserocr_segment_region_4.out[0], ocrd_tesserocr_segment_region_4.out[1], ocrd_tesserocr_segment_region_4.out[2], "OCR-D-SEG-BLOCK-TESSERACT", "OCR-D-SEGMENT-REPAIR")
+        ocrd_cis_ocropy_clip_6(ocrd_segment_repair_5.out[0], ocrd_segment_repair_5.out[1], ocrd_segment_repair_5.out[2], "OCR-D-SEGMENT-REPAIR", "OCR-D-CLIP")
+        ocrd_cis_ocropy_segment_7(ocrd_cis_ocropy_clip_6.out[0], ocrd_cis_ocropy_clip_6.out[1], ocrd_cis_ocropy_clip_6.out[2], "OCR-D-CLIP", "OCR-D-SEGMENT-OCROPY")
+        ocrd_cis_ocropy_dewarp_8(ocrd_cis_ocropy_segment_7.out[0], ocrd_cis_ocropy_segment_7.out[1], ocrd_cis_ocropy_segment_7.out[2], "OCR-D-SEGMENT-OCROPY", "OCR-D-DEWARP")
+        ocrd_tesserocr_recognize_9(ocrd_cis_ocropy_dewarp_8.out[0], ocrd_cis_ocropy_dewarp_8.out[1], ocrd_cis_ocropy_dewarp_8.out[2], "OCR-D-DEWARP", "OCR-D-OCR")
         merging_mets(ocrd_tesserocr_recognize_9.out[0], ocrd_tesserocr_recognize_9.out[1])
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
index a3235f59..240ae719 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
@@ -1,257 +1,301 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
-params.mets_socket = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
+params.mets_socket_path = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - Odem Workflow with Mets Server
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    mets_socket         : ${params.mets_socket}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
+params.env_wrapper_cmd_step1 = "null"
+params.env_wrapper_cmd_step2 = "null"
+params.env_wrapper_cmd_step3 = "null"
+params.env_wrapper_cmd_step4 = "null"
+params.env_wrapper_cmd_step5 = "null"
+params.env_wrapper_cmd_step6 = "null"
+params.env_wrapper_cmd_step7 = "null"
+params.env_wrapper_cmd_step8 = "null"
+params.env_wrapper_cmd_step9 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
+        env mets_file_chunk
         env current_range_pages
-    shell:
-    '''
-    current_range_pages=$(!{params.singularity_wrapper} ocrd workspace -d !{params.workspace_dir} list-page -f comma-separated -D !{params.forks} -C !{range_multiplier})
-    echo "Current range is: $current_range_pages"
-    '''
+
+    script:
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
+        """
 }
 
 process ocrd_cis_ocropy_binarize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-binarize -U ${params.mets_socket} -w ${params.workspace_dir} --page-id ${page_range} -m ${params.mets} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_anybaseocr_crop_1 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-anybaseocr-crop -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step1} ocrd-anybaseocr-crop -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_cis_ocropy_denoise_2 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-denoise -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step2} ocrd-cis-ocropy-denoise -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_cis_ocropy_deskew_3 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-deskew -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation page
-    """
+        """
+        ${params.env_wrapper_cmd_step3} ocrd-cis-ocropy-deskew -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+        """
 }
 
 process ocrd_tesserocr_segment_region_4 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-segment-region -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P padding 5.0 -P find_tables false -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step4} ocrd-tesserocr-segment-region -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"padding": 5.0, "find_tables": false, "dpi": 300}'
+        """
 }
 
 process ocrd_segment_repair_5 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-segment-repair -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P plausibilize true -P plausibilize_merge_min_overlap 0.7
-    """
+        """
+        ${params.env_wrapper_cmd_step5} ocrd-segment-repair -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"plausibilize": true, "plausibilize_merge_min_overlap": 0.7}'
+        """
 }
 
 process ocrd_cis_ocropy_clip_6 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-clip -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step6} ocrd-cis-ocropy-clip -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
 process ocrd_cis_ocropy_segment_7 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P dpi 300
-    """
+        """
+        ${params.env_wrapper_cmd_step7} ocrd-cis-ocropy-segment -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"dpi": 300}'
+        """
 }
 
 process ocrd_cis_ocropy_dewarp_8 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-dewarp -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step8} ocrd-cis-ocropy-dewarp -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
 process ocrd_tesserocr_recognize_9 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
+        val mets_path
         val page_range
+        val workspace_dir
 
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-recognize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P model Fraktur
-    """
+        """
+        ${params.env_wrapper_cmd_step9} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"model": "Fraktur"}'
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out, params.input_file_group, "OCR-D-BINPAGE")
-        ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out, "OCR-D-BINPAGE", "OCR-D-SEG-PAGE-ANYOCR")
-        ocrd_cis_ocropy_denoise_2(ocrd_anybaseocr_crop_1.out, "OCR-D-SEG-PAGE-ANYOCR", "OCR-D-DENOISE-OCROPY")
-        ocrd_cis_ocropy_deskew_3(ocrd_cis_ocropy_denoise_2.out, "OCR-D-DENOISE-OCROPY", "OCR-D-DESKEW-OCROPY")
-        ocrd_tesserocr_segment_region_4(ocrd_cis_ocropy_deskew_3.out, "OCR-D-DESKEW-OCROPY", "OCR-D-SEG-BLOCK-TESSERACT")
-        ocrd_segment_repair_5(ocrd_tesserocr_segment_region_4.out, "OCR-D-SEG-BLOCK-TESSERACT", "OCR-D-SEGMENT-REPAIR")
-        ocrd_cis_ocropy_clip_6(ocrd_segment_repair_5.out, "OCR-D-SEGMENT-REPAIR", "OCR-D-CLIP")
-        ocrd_cis_ocropy_segment_7(ocrd_cis_ocropy_clip_6.out, "OCR-D-CLIP", "OCR-D-SEGMENT-OCROPY")
-        ocrd_cis_ocropy_dewarp_8(ocrd_cis_ocropy_segment_7.out, "OCR-D-SEGMENT-OCROPY", "OCR-D-DEWARP")
-        ocrd_tesserocr_recognize_9(ocrd_cis_ocropy_dewarp_8.out, "OCR-D-DEWARP", "OCR-D-OCR")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BINPAGE")
+        ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BINPAGE", "OCR-D-SEG-PAGE-ANYOCR")
+        ocrd_cis_ocropy_denoise_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-SEG-PAGE-ANYOCR", "OCR-D-DENOISE-OCROPY")
+        ocrd_cis_ocropy_deskew_3(ocrd_cis_ocropy_denoise_2.out[0], ocrd_cis_ocropy_denoise_2.out[1], ocrd_cis_ocropy_denoise_2.out[2], "OCR-D-DENOISE-OCROPY", "OCR-D-DESKEW-OCROPY")
+        ocrd_tesserocr_segment_region_4(ocrd_cis_ocropy_deskew_3.out[0], ocrd_cis_ocropy_deskew_3.out[1], ocrd_cis_ocropy_deskew_3.out[2], "OCR-D-DESKEW-OCROPY", "OCR-D-SEG-BLOCK-TESSERACT")
+        ocrd_segment_repair_5(ocrd_tesserocr_segment_region_4.out[0], ocrd_tesserocr_segment_region_4.out[1], ocrd_tesserocr_segment_region_4.out[2], "OCR-D-SEG-BLOCK-TESSERACT", "OCR-D-SEGMENT-REPAIR")
+        ocrd_cis_ocropy_clip_6(ocrd_segment_repair_5.out[0], ocrd_segment_repair_5.out[1], ocrd_segment_repair_5.out[2], "OCR-D-SEGMENT-REPAIR", "OCR-D-CLIP")
+        ocrd_cis_ocropy_segment_7(ocrd_cis_ocropy_clip_6.out[0], ocrd_cis_ocropy_clip_6.out[1], ocrd_cis_ocropy_clip_6.out[2], "OCR-D-CLIP", "OCR-D-SEGMENT-OCROPY")
+        ocrd_cis_ocropy_dewarp_8(ocrd_cis_ocropy_segment_7.out[0], ocrd_cis_ocropy_segment_7.out[1], ocrd_cis_ocropy_segment_7.out[2], "OCR-D-SEGMENT-OCROPY", "OCR-D-DEWARP")
+        ocrd_tesserocr_recognize_9(ocrd_cis_ocropy_dewarp_8.out[0], ocrd_cis_ocropy_dewarp_8.out[1], ocrd_cis_ocropy_dewarp_8.out[2], "OCR-D-DEWARP", "OCR-D-OCR")
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf
index 4230534d..b7d3a235 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf
@@ -1,95 +1,86 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - SBB Workflow
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
         env mets_file_chunk
         env current_range_pages
+
     script:
-    """
-    current_range_pages=\$(${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
-    echo "Current range is: \$current_range_pages"
-    mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
-    echo "Mets file chunk path: \$mets_file_chunk"
-    \$(${params.singularity_wrapper} cp -p ${params.mets} \$mets_file_chunk)
-    """
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
+        echo "Mets file chunk path: \$mets_file_chunk"
+        \$(${params.env_wrapper_cmd_core} cp -p ${params.mets_path} \$mets_file_chunk)
+        """
 }
 
-process ocrd_tesserocr_recognize {
+process ocrd_tesserocr_recognize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-recognize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P segmentation_level region -P textequiv_level word -P find_tables true -P model deu
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"segmentation_level": "region", "textequiv_level": "word", "find_tables": true, "model": "deu"}'
+        """
 }
 
 process merging_mets {
-    // Must be a single instance - modifying the main mets file
+    debug true
     maxForks 1
+    cpus params.cpus_per_fork
+    memory params.ram_per_fork
 
     input:
         val mets_file_chunk
         val page_range
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
-    ${params.singularity_wrapper} rm ${mets_file_chunk}
-    """
+        """
+        ${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
+        ${params.env_wrapper_cmd_core} rm ${mets_file_chunk}
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_tesserocr_recognize(split_page_ranges.out[0], split_page_ranges.out[1], params.input_file_group, "OCR-D-OCR")
-        merging_mets(ocrd_tesserocr_recognize.out[0], ocrd_tesserocr_recognize.out[1])
+        ocrd_tesserocr_recognize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-OCR")
+        merging_mets(ocrd_tesserocr_recognize_0.out[0], ocrd_tesserocr_recognize_0.out[1])
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf
index 9c24f34b..389772b5 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf
@@ -1,74 +1,67 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
-params.mets_socket = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
+params.mets_socket_path = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - SBB Workflow with Mets Server
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    mets_socket         : ${params.mets_socket}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
+        env mets_file_chunk
         env current_range_pages
-    shell:
-    '''
-    current_range_pages=$(!{params.singularity_wrapper} ocrd workspace -d !{params.workspace_dir} list-page -f comma-separated -D !{params.forks} -C !{range_multiplier})
-    echo "Current range is: $current_range_pages"
-    '''
+
+    script:
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
+        """
 }
 
-process ocrd_tesserocr_recognize {
+process ocrd_tesserocr_recognize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
+    output:
+        val mets_path
+        val page_range
+        val workspace_dir
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd-tesserocr-recognize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P segmentation_level region -P textequiv_level word -P find_tables true -P model deu
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-tesserocr-recognize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group} -p '{"segmentation_level": "region", "textequiv_level": "word", "find_tables": true, "model": "deu"}'
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_tesserocr_recognize(split_page_ranges.out[0], params.input_file_group, "OCR-D-BIN")
+        ocrd_tesserocr_recognize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-OCR")
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf
index bb001c6d..fc01fceb 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf
@@ -1,95 +1,86 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - Template Workflow
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
         env mets_file_chunk
         env current_range_pages
+
     script:
-    """
-    current_range_pages=\$(${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
-    echo "Current range is: \$current_range_pages"
-    mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
-    echo "Mets file chunk path: \$mets_file_chunk"
-    \$(${params.singularity_wrapper} cp -p ${params.mets} \$mets_file_chunk)
-    """
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.workspace_dir}/mets_${range_multiplier}.xml)
+        echo "Mets file chunk path: \$mets_file_chunk"
+        \$(${params.env_wrapper_cmd_core} cp -p ${params.mets_path} \$mets_file_chunk)
+        """
 }
 
-process ocrd_cis_ocropy_binarize {
+process ocrd_cis_ocropy_binarize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
     output:
-        val mets_file_chunk
+        val mets_path
         val page_range
+        val workspace_dir
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-binarize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
 process merging_mets {
-    // Must be a single instance - modifying the main mets file
+    debug true
     maxForks 1
+    cpus params.cpus_per_fork
+    memory params.ram_per_fork
 
     input:
         val mets_file_chunk
         val page_range
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
-    ${params.singularity_wrapper} rm ${mets_file_chunk}
-    """
+        """
+        ${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} merge --force --no-copy-files ${mets_file_chunk} --page-id ${page_range}
+        ${params.env_wrapper_cmd_core} rm ${mets_file_chunk}
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize(split_page_ranges.out[0], split_page_ranges.out[1], params.input_file_group, "OCR-D-BIN")
-        merging_mets(ocrd_cis_ocropy_binarize.out[0], ocrd_cis_ocropy_binarize.out[1])
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
+        merging_mets(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1])
 }
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf
index d89e8ee3..be041784 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf
@@ -1,74 +1,67 @@
-nextflow.enable.dsl=2
+// This workflow was automatically generated by the v2.17.0 operandi_utils.oton module
+nextflow.enable.dsl = 2
 
-// The values are assigned inside the batch script
-// Based on internal values and options provided in the request
-params.input_file_group = "null"
-params.mets = "null"
-params.mets_socket = "null"
+params.input_file_group = "OCR-D-IMG"
+params.mets_path = "null"
 params.workspace_dir = "null"
-// amount of pages of the workspace
 params.pages = "null"
-params.singularity_wrapper = "null"
+params.mets_socket_path = "null"
 params.cpus = "null"
 params.ram = "null"
 params.forks = params.cpus
-// Do not pass these parameters from the caller unless you know what you are doing
 params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()
 params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())
-
-log.info """\
-    OPERANDI - HPC - Template Workflow with Mets Server
-    ===========================================
-    input_file_group    : ${params.input_file_group}
-    mets                : ${params.mets}
-    mets_socket         : ${params.mets_socket}
-    workspace_dir       : ${params.workspace_dir}
-    pages               : ${params.pages}
-    singularity_wrapper : ${params.singularity_wrapper}
-    cpus                : ${params.cpus}
-    ram                 : ${params.ram}
-    forks               : ${params.forks}
-    cpus_per_fork       : ${params.cpus_per_fork}
-    ram_per_fork        : ${params.ram_per_fork}
-    """
-    .stripIndent()
+params.env_wrapper_cmd_core = "null"
+params.env_wrapper_cmd_step0 = "null"
 
 process split_page_ranges {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
         val range_multiplier
+
     output:
+        env mets_file_chunk
         env current_range_pages
-    shell:
-    '''
-    current_range_pages=$(!{params.singularity_wrapper} ocrd workspace -d !{params.workspace_dir} list-page -f comma-separated -D !{params.forks} -C !{range_multiplier})
-    echo "Current range is: $current_range_pages"
-    '''
+
+    script:
+        """
+        current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
+        echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
+        """
 }
 
-process ocrd_cis_ocropy_binarize {
+process ocrd_cis_ocropy_binarize_0 {
+    debug true
     maxForks params.forks
     cpus params.cpus_per_fork
     memory params.ram_per_fork
-    debug true
 
     input:
+        val mets_path
         val page_range
+        val workspace_dir
         val input_group
         val output_group
+
+    output:
+        val mets_path
+        val page_range
+        val workspace_dir
+
     script:
-    """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-binarize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group}
-    """
+        """
+        ${params.env_wrapper_cmd_step0} ocrd-cis-ocropy-binarize -w ${workspace_dir} -m ${mets_path} -I ${input_group} -O ${output_group}
+        """
 }
 
 workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize(split_page_ranges.out[0], params.input_file_group, "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
 }
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index 1684dc9b..b278d1ef 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -3,6 +3,7 @@
 from os.path import join
 from pathlib import Path
 from time import sleep
+from typing import List
 
 from operandi_utils.constants import StateJobSlurm
 from .constants import (
@@ -37,8 +38,9 @@ def execute_blocking(self, command, timeout=None, environment=None):
     def trigger_slurm_job(
         self, workflow_job_id: str, nextflow_script_path: Path, input_file_grp: str,
         workspace_id: str, mets_basename: str, nf_process_forks: int, ws_pages_amount: int, use_mets_server: bool,
-        file_groups_to_remove: str, cpus: int = 2, ram: int = 8, job_deadline_time: str = HPC_JOB_DEADLINE_TIME_TEST,
-        partition: str = HPC_NHR_JOB_DEFAULT_PARTITION, qos: str = HPC_JOB_QOS_DEFAULT
+        nf_executable_steps: List[str], file_groups_to_remove: str, cpus: int = 2, ram: int = 8,
+        job_deadline_time: str = HPC_JOB_DEADLINE_TIME_TEST, partition: str = HPC_NHR_JOB_DEFAULT_PARTITION,
+        qos: str = HPC_JOB_QOS_DEFAULT
     ) -> str:
         if ws_pages_amount < nf_process_forks:
             self.logger.warning(
@@ -74,7 +76,8 @@ def trigger_slurm_job(
             hpc_nf_script_path=hpc_nf_script_path, hpc_ws_dir=hpc_workspace_dir,
             bind_ocrd_models=f"{ph_node_dir_ocrd_models}/ocrd-resources:/usr/local/share/ocrd-resources",
             ph_sif_ocrd_all=ph_node_sif_path_ocrd_all, input_file_grp=input_file_grp, mets_basename=mets_basename,
-            use_mets_server=use_mets_server, ws_pages_amount=ws_pages_amount, cpus=cpus, ram=ram, forks=nf_process_forks
+            use_mets_server=use_mets_server, nf_executable_steps=nf_executable_steps, ws_pages_amount=ws_pages_amount,
+            cpus=cpus, ram=ram, forks=nf_process_forks
         )
 
         regular_args = {
@@ -174,21 +177,27 @@ def poll_till_end_slurm_job_state(self, slurm_job_id: str, interval: int = 5, ti
     @staticmethod
     def cmd_nextflow_run(
         hpc_nf_script_path: str, hpc_ws_dir: str, bind_ocrd_models: str, ph_sif_ocrd_all: str, input_file_grp: str,
-        mets_basename: str, use_mets_server: bool, ws_pages_amount: int, cpus: int, ram: int, forks: int
+        mets_basename: str, use_mets_server: bool, nf_executable_steps: List[str], ws_pages_amount: int, cpus: int,
+        ram: int, forks: int
     ) -> str:
-        apptainer_cmd = f"apptainer exec --bind {hpc_ws_dir}:/ws_data --bind {bind_ocrd_models}"
-        apptainer_cmd += f" --env OCRD_METS_CACHING=false {ph_sif_ocrd_all}"
-
         nf_run_command = f"nextflow run {hpc_nf_script_path} -ansi-log false -with-report"
         nf_run_command += f" --input_file_group {input_file_grp}"
-        nf_run_command += f" --mets /ws_data/{mets_basename}"
+        nf_run_command += f" --mets_path /ws_data/{mets_basename}"
         if use_mets_server:
             nf_run_command += f" --mets_socket /ws_data/mets_server.sock"
         nf_run_command += f" --workspace_dir /ws_data"
         nf_run_command += f" --pages {ws_pages_amount}"
         # Command wrapper placeholder. Each occurrence is replaced with a single quote ' to avoid json parsing errors
+
+        # TODO: Send actual slim image apptainer cmds here instead of the sif_ocrd_all
         ph_cmd_wrapper = "PH_CMD_WRAPPER"
-        nf_run_command += f" --singularity_wrapper {ph_cmd_wrapper}{apptainer_cmd}{ph_cmd_wrapper}"
+        index = 0
+        apptainer_cmd = f"apptainer exec --bind {hpc_ws_dir}:/ws_data --bind {bind_ocrd_models}"
+        apptainer_cmd += f" --env OCRD_METS_CACHING=false {ph_sif_ocrd_all}"
+        nf_run_command += f" --env_wrapper_cmd_core {ph_cmd_wrapper}{apptainer_cmd}{ph_cmd_wrapper}"
+        for executable_step in nf_executable_steps:
+            nf_run_command += f" --env_wrapper_cmd_step{index} {ph_cmd_wrapper}{apptainer_cmd}{ph_cmd_wrapper}"
+            index += 1
         nf_run_command += f" --cpus {cpus}"
         nf_run_command += f" --ram {ram}"
         nf_run_command += f" --forks {forks}"
diff --git a/src/utils/operandi_utils/hpc/ocrd_process_workflows/default_workflow.txt b/src/utils/operandi_utils/hpc/ocrd_process_workflows/default_workflow.txt
new file mode 100644
index 00000000..b6374302
--- /dev/null
+++ b/src/utils/operandi_utils/hpc/ocrd_process_workflows/default_workflow.txt
@@ -0,0 +1,9 @@
+ocrd process \
+    "cis-ocropy-binarize -I OCR-D-IMG -O OCR-D-BIN" \
+    "anybaseocr-crop -I OCR-D-BIN -O OCR-D-CROP" \
+    "skimage-binarize -I OCR-D-CROP -O OCR-D-BIN2 -P method li" \
+    "skimage-denoise -I OCR-D-BIN2 -O OCR-D-BIN-DENOISE -P level-of-operation page" \
+    "tesserocr-deskew -I OCR-D-BIN-DENOISE -O OCR-D-BIN-DENOISE-DESKEW -P operation_level page" \
+    "cis-ocropy-segment -I OCR-D-BIN-DENOISE-DESKEW -O OCR-D-SEG -P level-of-operation page" \
+    "cis-ocropy-dewarp -I OCR-D-SEG -O OCR-D-SEG-LINE-RESEG-DEWARP" \
+    "calamari-recognize -I OCR-D-SEG-LINE-RESEG-DEWARP -O OCR-D-OCR -P checkpoint_dir qurator-gt4histocr-1.0"
diff --git a/src/utils/operandi_utils/hpc/ocrd_process_workflows/odem_workflow.txt b/src/utils/operandi_utils/hpc/ocrd_process_workflows/odem_workflow.txt
new file mode 100644
index 00000000..63d8e7bb
--- /dev/null
+++ b/src/utils/operandi_utils/hpc/ocrd_process_workflows/odem_workflow.txt
@@ -0,0 +1,11 @@
+ocrd process \
+	"cis-ocropy-binarize -I OCR-D-IMG -O OCR-D-BINPAGE -P dpi 300" \
+	"anybaseocr-crop -I OCR-D-BINPAGE -O OCR-D-SEG-PAGE-ANYOCR -P dpi 300" \
+	"cis-ocropy-denoise -I OCR-D-SEG-PAGE-ANYOCR -O OCR-D-DENOISE-OCROPY -P dpi 300" \
+	"cis-ocropy-deskew -I OCR-D-DENOISE-OCROPY -O OCR-D-DESKEW-OCROPY -P level-of-operation page" \
+	"tesserocr-segment-region -I OCR-D-DESKEW-OCROPY -O OCR-D-SEG-BLOCK-TESSERACT -P padding 5.0 -P find_tables false -P dpi 300" \
+	"segment-repair -I OCR-D-SEG-BLOCK-TESSERACT -O OCR-D-SEGMENT-REPAIR -P plausibilize true -P plausibilize_merge_min_overlap 0.7" \
+	"cis-ocropy-clip -I OCR-D-SEGMENT-REPAIR -O OCR-D-CLIP" \
+	"cis-ocropy-segment -I OCR-D-CLIP -O OCR-D-SEGMENT-OCROPY -P dpi 300" \
+	"cis-ocropy-dewarp -I OCR-D-SEGMENT-OCROPY -O OCR-D-DEWARP" \
+	"tesserocr-recognize -I OCR-D-DEWARP -O OCR-D-OCR -P model Fraktur"
diff --git a/src/utils/operandi_utils/hpc/ocrd_process_workflows/sbb_workflow.txt b/src/utils/operandi_utils/hpc/ocrd_process_workflows/sbb_workflow.txt
new file mode 100644
index 00000000..49cdd8ad
--- /dev/null
+++ b/src/utils/operandi_utils/hpc/ocrd_process_workflows/sbb_workflow.txt
@@ -0,0 +1,2 @@
+ocrd process \
+    "tesserocr-recognize -I OCR-D-IMG -O OCR-D-OCR -P segmentation_level region -P textequiv_level word -P find_tables true -P model deu"
diff --git a/src/utils/operandi_utils/hpc/ocrd_process_workflows/template_workflow.txt b/src/utils/operandi_utils/hpc/ocrd_process_workflows/template_workflow.txt
new file mode 100644
index 00000000..2bbc6cda
--- /dev/null
+++ b/src/utils/operandi_utils/hpc/ocrd_process_workflows/template_workflow.txt
@@ -0,0 +1,2 @@
+ocrd process \
+    "cis-ocropy-binarize -I OCR-D-IMG -O OCR-D-BIN"
diff --git a/src/utils/operandi_utils/oton/nf_block_workflow.py b/src/utils/operandi_utils/oton/nf_block_workflow.py
index f6d17374..e37b64ec 100644
--- a/src/utils/operandi_utils/oton/nf_block_workflow.py
+++ b/src/utils/operandi_utils/oton/nf_block_workflow.py
@@ -37,7 +37,7 @@ def produce_workflow_calls(
             if previous_nfp is None:
                 workflow_call += (
                     f'{nf_split_page_ranges.nf_process_name}.out[0], {nf_split_page_ranges.nf_process_name}.out[1], '
-                    f'{PARAMS_KEY_WORKSPACE_DIR}, {PARAMS_KEY_INPUT_FILE_GRP} "{out_file_grps}"'
+                    f'{PARAMS_KEY_WORKSPACE_DIR}, {PARAMS_KEY_INPUT_FILE_GRP}, "{out_file_grps}"'
                 )
             else:
                 workflow_call += (
diff --git a/src/utils/operandi_utils/oton/nf_file_executable.py b/src/utils/operandi_utils/oton/nf_file_executable.py
index 43a94744..ef6b7529 100644
--- a/src/utils/operandi_utils/oton/nf_file_executable.py
+++ b/src/utils/operandi_utils/oton/nf_file_executable.py
@@ -85,8 +85,7 @@ def build_split_page_ranges_process(self, environment: str, with_mets_server: bo
             block.add_directive(directive='memory', value=PARAMS_KEY_RAM_PER_FORK)
 
         block.add_parameter_input(parameter="range_multiplier", parameter_type="val")
-        if not with_mets_server:
-            block.add_parameter_output(parameter="mets_file_chunk", parameter_type="env")
+        block.add_parameter_output(parameter="mets_file_chunk", parameter_type="env")
         block.add_parameter_output(parameter="current_range_pages", parameter_type="env")
 
         PH_RANGE_MULTIPLIER = '${range_multiplier}'
@@ -103,6 +102,9 @@ def build_split_page_ranges_process(self, environment: str, with_mets_server: bo
         script += f"{bash_cmd_ocrd_ws})\n"
         script += f'{SPACES}{SPACES}echo "Current range is: \\$current_range_pages"\n'
 
+        if with_mets_server:
+            script += f"{SPACES}{SPACES}mets_file_chunk=\\$(echo ${BS[0]}{PARAMS_KEY_METS_PATH}{BS[1]})\n"
+
         if not with_mets_server:
             script += f"{SPACES}{SPACES}mets_file_chunk=\\$(echo ${BS[0]}{PARAMS_KEY_WORKSPACE_DIR}{BS[1]}/mets_{PH_RANGE_MULTIPLIER}.xml)\n"
             script += f'{SPACES}{SPACES}echo "Mets file chunk path: \\$mets_file_chunk"\n'
diff --git a/src/utils/operandi_utils/utils.py b/src/utils/operandi_utils/utils.py
index b68bbfc3..c9a3cb1e 100644
--- a/src/utils/operandi_utils/utils.py
+++ b/src/utils/operandi_utils/utils.py
@@ -83,9 +83,11 @@ def is_url_responsive(url: str) -> bool:
         return False
 
 
-def get_nf_workflows_dir() -> Path:
+def get_nf_wfs_dir() -> Path:
     return Path(dirname(__file__), "hpc", "nextflow_workflows")
 
+def get_ocrd_process_wfs_dir() -> Path:
+    return Path(dirname(__file__), "hpc", "ocrd_process_workflows")
 
 def generate_id(file_ext: str = None):
     generated_id = str(uuid4())
diff --git a/tests/assets/oton/constants.py b/tests/assets/oton/constants.py
index 91404cda..b8f3e053 100644
--- a/tests/assets/oton/constants.py
+++ b/tests/assets/oton/constants.py
@@ -27,7 +27,7 @@
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
@@ -44,7 +44,7 @@
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
@@ -60,7 +60,7 @@
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_denoise_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN-DENOISE")
         ocrd_tesserocr_deskew_3(ocrd_skimage_denoise_2.out[0], ocrd_skimage_denoise_2.out[1], ocrd_skimage_denoise_2.out[2], "OCR-D-BIN-DENOISE", "OCR-D-BIN-DENOISE-DESKEW")
@@ -76,7 +76,7 @@
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_dinglehopper_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-EVAL-SEG-BLOCK")
+        ocrd_dinglehopper_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-EVAL-SEG-BLOCK")
         ocrd_dinglehopper_1(ocrd_dinglehopper_0.out[0], ocrd_dinglehopper_0.out[1], ocrd_dinglehopper_0.out[2], "OCR-D-GT-SEG-LINE,OCR-D-OCR", "OCR-D-EVAL-SEG-LINE")
         ocrd_dinglehopper_2(ocrd_dinglehopper_1.out[0], ocrd_dinglehopper_1.out[1], ocrd_dinglehopper_1.out[2], "OCR-D-GT-SEG-PAGE,OCR-D-OCR", "OCR-D-EVAL-SEG-PAGE")
         merging_mets(ocrd_dinglehopper_2.out[0], ocrd_dinglehopper_2.out[1])
@@ -88,7 +88,7 @@
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_olena_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_olena_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_olena_binarize_0.out[0], ocrd_olena_binarize_0.out[1], ocrd_olena_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_olena_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_cis_ocropy_denoise_3(ocrd_olena_binarize_2.out[0], ocrd_olena_binarize_2.out[1], ocrd_olena_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow1_apptainer.nf b/tests/assets/oton/test_output_nextflow1_apptainer.nf
index 836b69a0..b057341e 100644
--- a/tests/assets/oton/test_output_nextflow1_apptainer.nf
+++ b/tests/assets/oton/test_output_nextflow1_apptainer.nf
@@ -256,7 +256,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf b/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
index ce5de9c7..590ba3c4 100644
--- a/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
@@ -31,12 +31,14 @@ process split_page_ranges {
         val range_multiplier
 
     output:
+        env mets_file_chunk
         env current_range_pages
 
     script:
         """
         current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
         """
 }
 
@@ -236,7 +238,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow1_docker.nf b/tests/assets/oton/test_output_nextflow1_docker.nf
index aa10c21c..4f59235a 100644
--- a/tests/assets/oton/test_output_nextflow1_docker.nf
+++ b/tests/assets/oton/test_output_nextflow1_docker.nf
@@ -232,7 +232,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf b/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
index 870ea30c..105bd787 100644
--- a/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
@@ -25,12 +25,14 @@ process split_page_ranges {
         val range_multiplier
 
     output:
+        env mets_file_chunk
         env current_range_pages
 
     script:
         """
         current_range_pages=\$(${params.env_wrapper_cmd_core} ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
         """
 }
 
@@ -214,7 +216,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow1_local.nf b/tests/assets/oton/test_output_nextflow1_local.nf
index 0e2cafde..812258c8 100644
--- a/tests/assets/oton/test_output_nextflow1_local.nf
+++ b/tests/assets/oton/test_output_nextflow1_local.nf
@@ -231,7 +231,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow1_local_with_MS.nf b/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
index 8f2655cf..7685e74c 100644
--- a/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
@@ -24,12 +24,14 @@ process split_page_ranges {
         val range_multiplier
 
     output:
+        env mets_file_chunk
         env current_range_pages
 
     script:
         """
         current_range_pages=\$(ocrd workspace -d ${params.workspace_dir} list-page -f comma-separated -D ${params.forks} -C ${range_multiplier})
         echo "Current range is: \$current_range_pages"
+        mets_file_chunk=\$(echo ${params.mets_path})
         """
 }
 
@@ -213,7 +215,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_skimage_denoise_3(ocrd_skimage_binarize_2.out[0], ocrd_skimage_binarize_2.out[1], ocrd_skimage_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/assets/oton/test_output_nextflow2.nf b/tests/assets/oton/test_output_nextflow2.nf
index 43a633f9..a10ca1ad 100644
--- a/tests/assets/oton/test_output_nextflow2.nf
+++ b/tests/assets/oton/test_output_nextflow2.nf
@@ -208,7 +208,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_cis_ocropy_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_cis_ocropy_binarize_0.out[0], ocrd_cis_ocropy_binarize_0.out[1], ocrd_cis_ocropy_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_skimage_denoise_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN-DENOISE")
         ocrd_tesserocr_deskew_3(ocrd_skimage_denoise_2.out[0], ocrd_skimage_denoise_2.out[1], ocrd_skimage_denoise_2.out[2], "OCR-D-BIN-DENOISE", "OCR-D-BIN-DENOISE-DESKEW")
diff --git a/tests/assets/oton/test_output_nextflow3.nf b/tests/assets/oton/test_output_nextflow3.nf
index eaa7ab06..4e551f1e 100644
--- a/tests/assets/oton/test_output_nextflow3.nf
+++ b/tests/assets/oton/test_output_nextflow3.nf
@@ -116,7 +116,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_dinglehopper_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-EVAL-SEG-BLOCK")
+        ocrd_dinglehopper_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-EVAL-SEG-BLOCK")
         ocrd_dinglehopper_1(ocrd_dinglehopper_0.out[0], ocrd_dinglehopper_0.out[1], ocrd_dinglehopper_0.out[2], "OCR-D-GT-SEG-LINE,OCR-D-OCR", "OCR-D-EVAL-SEG-LINE")
         ocrd_dinglehopper_2(ocrd_dinglehopper_1.out[0], ocrd_dinglehopper_1.out[1], ocrd_dinglehopper_1.out[2], "OCR-D-GT-SEG-PAGE,OCR-D-OCR", "OCR-D-EVAL-SEG-PAGE")
         merging_mets(ocrd_dinglehopper_2.out[0], ocrd_dinglehopper_2.out[1])
diff --git a/tests/assets/oton/test_output_nextflow4.nf b/tests/assets/oton/test_output_nextflow4.nf
index e1138699..1d4f600b 100644
--- a/tests/assets/oton/test_output_nextflow4.nf
+++ b/tests/assets/oton/test_output_nextflow4.nf
@@ -346,7 +346,7 @@ workflow {
     main:
         ch_range_multipliers = Channel.of(0..params.forks.intValue()-1)
         split_page_ranges(ch_range_multipliers)
-        ocrd_olena_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group "OCR-D-BIN")
+        ocrd_olena_binarize_0(split_page_ranges.out[0], split_page_ranges.out[1], params.workspace_dir, params.input_file_group, "OCR-D-BIN")
         ocrd_anybaseocr_crop_1(ocrd_olena_binarize_0.out[0], ocrd_olena_binarize_0.out[1], ocrd_olena_binarize_0.out[2], "OCR-D-BIN", "OCR-D-CROP")
         ocrd_olena_binarize_2(ocrd_anybaseocr_crop_1.out[0], ocrd_anybaseocr_crop_1.out[1], ocrd_anybaseocr_crop_1.out[2], "OCR-D-CROP", "OCR-D-BIN2")
         ocrd_cis_ocropy_denoise_3(ocrd_olena_binarize_2.out[0], ocrd_olena_binarize_2.out[1], ocrd_olena_binarize_2.out[2], "OCR-D-BIN2", "OCR-D-BIN-DENOISE")
diff --git a/tests/tests_server/test_endpoint_workflow.py b/tests/tests_server/test_endpoint_workflow.py
index 1b812806..2fc107c8 100644
--- a/tests/tests_server/test_endpoint_workflow.py
+++ b/tests/tests_server/test_endpoint_workflow.py
@@ -3,8 +3,20 @@
 from tests.constants import WORKFLOW_DUMMY_TEXT
 from .helpers_asserts import assert_local_dir_workflow, assert_response_status_code
 
+def test_post_workflow_script(operandi, auth, db_workflows, bytes_template_workflow):
+    # Post a new workflow script
+    wf_detail = "Test template workflow with mets server"
+    response = operandi.post(
+        url=f"/workflow?details={wf_detail}", files={"nextflow_script": bytes_template_workflow}, auth=auth)
+    assert_response_status_code(response.status_code, expected_floor=2)
+    workflow_id = response.json()['resource_id']
+    assert_local_dir_workflow(workflow_id)
+    db_workflow = db_workflows.find_one({"workflow_id": workflow_id})
+    assert_exists_db_resource(db_workflow, resource_key="workflow_id", resource_id=workflow_id)
+    assert db_workflow["details"] == wf_detail
+    assert db_workflow["uses_mets_server"] == False
 
-def test_post_workflow_script(operandi, auth, db_workflows, bytes_template_workflow_with_ms):
+def test_post_workflow_script_with_ms(operandi, auth, db_workflows, bytes_template_workflow_with_ms):
     # Post a new workflow script
     wf_detail = "Test template workflow with mets server"
     response = operandi.post(
@@ -15,6 +27,7 @@ def test_post_workflow_script(operandi, auth, db_workflows, bytes_template_workf
     db_workflow = db_workflows.find_one({"workflow_id": workflow_id})
     assert_exists_db_resource(db_workflow, resource_key="workflow_id", resource_id=workflow_id)
     assert db_workflow["details"] == wf_detail
+    assert db_workflow["uses_mets_server"] == True
 
 
 def test_put_workflow_script(
@@ -38,6 +51,7 @@ def test_put_workflow_script(
     assert workflow_path1, "Failed to extract workflow path 1"
     assert workflow_details1, "Failed to extract workflow details 1"
     assert db_workflow["details"] == wf_detail
+    assert db_workflow["uses_mets_server"] == True
 
     # The second put request replaces the previously created workflow
     files = {"nextflow_script": bytes_default_workflow_with_ms}
@@ -56,6 +70,7 @@ def test_put_workflow_script(
     assert workflow_path2, "Failed to extract workflow path 2"
     assert workflow_details2, "Failed to extract workflow details 2"
     assert db_workflow["details"] == wf_detail_put
+    assert db_workflow["uses_mets_server"] == True
 
     assert workflow_dir1 == workflow_dir2, \
         f"Workflow dir paths should match, but does not: {workflow_dir1} != {workflow_dir2}"
diff --git a/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py b/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
index 2ba80b1d..35d5cc46 100644
--- a/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
+++ b/tests/tests_utils/test_3_hpc/test_1_nhr_executor.py
@@ -6,7 +6,7 @@
 
 
 def test_hpc_connector_executor_mk_dir(hpc_nhr_command_executor):
-    test_dir_name = join(hpc_nhr_command_executor.project_root_dir, f"test_dir_{current_time}")
+    test_dir_name = join(hpc_nhr_command_executor.project_root_dir_with_env, f"test_dir_{current_time}")
     sleep(0.5)
     output, err, return_code = hpc_nhr_command_executor.execute_blocking(command=f"bash -lc 'mkdir -p {test_dir_name}'")
     assert return_code == 0, err
@@ -15,7 +15,7 @@ def test_hpc_connector_executor_mk_dir(hpc_nhr_command_executor):
 
 
 def test_hpc_connector_executor_rm_dir_negative(hpc_nhr_command_executor):
-    test_dir_name = join(hpc_nhr_command_executor.project_root_dir, f"test_dir_{current_time}")
+    test_dir_name = join(hpc_nhr_command_executor.project_root_dir_with_env, f"test_dir_{current_time}")
     sleep(0.5)
     output, err, return_code = hpc_nhr_command_executor.execute_blocking(command=f"bash -lc 'rm {test_dir_name}'")
     assert return_code == 1
@@ -25,7 +25,7 @@ def test_hpc_connector_executor_rm_dir_negative(hpc_nhr_command_executor):
 
 
 def test_hpc_connector_executor_rm_dir_positive(hpc_nhr_command_executor):
-    test_dir_name = join(hpc_nhr_command_executor.project_root_dir, f"test_dir_{current_time}")
+    test_dir_name = join(hpc_nhr_command_executor.project_root_dir_with_env, f"test_dir_{current_time}")
     sleep(0.5)
     output, err, return_code = hpc_nhr_command_executor.execute_blocking(command=f"bash -lc 'rm -rf {test_dir_name}'")
     assert return_code == 0
@@ -34,7 +34,7 @@ def test_hpc_connector_executor_rm_dir_positive(hpc_nhr_command_executor):
 
 
 def test_hpc_connector_executor_cd_dir(hpc_nhr_command_executor):
-    test_dir_name = join(hpc_nhr_command_executor.project_root_dir, f"test_dir_{current_time}")
+    test_dir_name = join(hpc_nhr_command_executor.project_root_dir_with_env, f"test_dir_{current_time}")
     sleep(0.5)
     output, err, return_code = hpc_nhr_command_executor.execute_blocking(command=f"bash -lc 'cd {test_dir_name}'")
     assert return_code == 1
diff --git a/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py b/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
index 3a81b884..be740443 100644
--- a/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
+++ b/tests/tests_utils/test_3_hpc/test_2_nhr_transfer.py
@@ -15,7 +15,7 @@ def test_hpc_connector_transfer_file(hpc_nhr_data_transfer, path_batch_script_em
     """
     assert_exists_file(str(path_batch_script_empty))
 
-    test_hpc_file_path = Path(hpc_nhr_data_transfer.project_root_dir, BATCH_SCRIPT_EMPTY)
+    test_hpc_file_path = Path(hpc_nhr_data_transfer.project_root_dir_with_env, BATCH_SCRIPT_EMPTY)
     hpc_nhr_data_transfer.put_file(local_src=path_batch_script_empty, remote_dst=str(test_hpc_file_path))
     sleep(2)
     test_local_received_file_path = Path(OPERANDI_SERVER_BASE_DIR, BATCH_SCRIPT_EMPTY)
@@ -29,7 +29,7 @@ def test_hpc_connector_transfer_dir(hpc_nhr_data_transfer, path_dummy_workspace_
     Testing the put_dir and get_dir functionality of the HPC transfer
     """
     assert_exists_dir(str(path_dummy_workspace_data_dir))
-    test_hpc_dir_path = Path(hpc_nhr_data_transfer.project_root_dir, ID_WORKSPACE)
+    test_hpc_dir_path = Path(hpc_nhr_data_transfer.project_root_dir_with_env, ID_WORKSPACE)
     hpc_nhr_data_transfer.put_dir(local_src=str(path_dummy_workspace_data_dir), remote_dst=str(test_hpc_dir_path))
     sleep(5)
     test_local_received_dir_path = Path(OPERANDI_SERVER_BASE_DIR, ID_WORKSPACE)
diff --git a/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
index 3309b538..c584386d 100644
--- a/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
+++ b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
@@ -56,12 +56,13 @@ def test_pack_and_put_slurm_workspace_with_ms(
     )
 
 
-def test_hpc_connector_run_batch_script(
+def _test_hpc_connector_run_batch_script(
     hpc_nhr_command_executor, hpc_nhr_data_transfer, template_workflow):
     slurm_job_id = hpc_nhr_command_executor.trigger_slurm_job(
         workflow_job_id=ID_WORKFLOW_JOB, nextflow_script_path=Path(template_workflow),
         input_file_grp=DEFAULT_FILE_GRP, workspace_id=ID_WORKSPACE,
-        mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8, use_mets_server=False,
+        mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8,
+        use_mets_server=False, nf_executable_steps=["ocrd-cis-ocropy-binarize"],
         file_groups_to_remove="", cpus=2, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
         partition=HPC_NHR_JOB_TEST_PARTITION, qos=HPC_JOB_QOS_SHORT)
     finished_successfully = hpc_nhr_command_executor.poll_till_end_slurm_job_state(
@@ -84,7 +85,8 @@ def test_hpc_connector_run_batch_script_with_ms(
         workflow_job_id=ID_WORKFLOW_JOB_WITH_MS, nextflow_script_path=Path(template_workflow_with_ms),
         input_file_grp=DEFAULT_FILE_GRP, workspace_id=ID_WORKSPACE_WITH_MS,
         mets_basename=DEFAULT_METS_BASENAME, nf_process_forks=2, ws_pages_amount=8,
-        use_mets_server=True, file_groups_to_remove="", cpus=3, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
+        use_mets_server=True, nf_executable_steps=["ocrd-cis-ocropy-binarize"],
+        file_groups_to_remove="", cpus=3, ram=16, job_deadline_time=HPC_JOB_DEADLINE_TIME_TEST,
         partition=HPC_NHR_JOB_TEST_PARTITION, qos=HPC_JOB_QOS_SHORT)
     finished_successfully = hpc_nhr_command_executor.poll_till_end_slurm_job_state(
         slurm_job_id=slurm_job_id, interval=5, timeout=300)

From b3e70260ae31e15127b80c40dca96a858a137bf2 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Fri, 29 Nov 2024 16:58:28 +0100
Subject: [PATCH 10/16] add: extra logging when oton converting

---
 src/server/operandi_server/routers/workflow.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/server/operandi_server/routers/workflow.py b/src/server/operandi_server/routers/workflow.py
index 5a7a1121..5bf43374 100644
--- a/src/server/operandi_server/routers/workflow.py
+++ b/src/server/operandi_server/routers/workflow.py
@@ -149,12 +149,15 @@ async def produce_production_workflows(
                 continue
             # path.stem -> file_name
             # path.name -> file_name.ext
+            self.logger.info(f"Converting to Nextflow workflow the ocrd process workflow: {path}")
             output_path = Path(production_nf_wfs_dir, f"{path.stem}.nf")
             oton_converter.convert_oton(
                 input_path=path, output_path=str(output_path), environment="apptainer", with_mets_server=False)
+            self.logger.info(f"Converted to a Nextflow file without a mets server: {output_path}")
             output_path = Path(production_nf_wfs_dir, f"{path.stem}_with_MS.nf")
             oton_converter.convert_oton(
                 input_path=path, output_path=str(output_path), environment="apptainer", with_mets_server=True)
+            self.logger.info(f"Converted to a Nextflow file with a mets server: {output_path}")
 
     async def insert_production_workflows(self, production_nf_wfs_dir: Path = get_nf_wfs_dir()):
         wf_detail = "Workflow provided by the Operandi Server"

From 3a5658828a410378c0c67d6009b75156799270a6 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Fri, 29 Nov 2024 17:13:22 +0100
Subject: [PATCH 11/16] fix: processor executables entry in the DBWorkflow

---
 src/server/operandi_server/routers/workflow_utils.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/server/operandi_server/routers/workflow_utils.py b/src/server/operandi_server/routers/workflow_utils.py
index 39a837fa..591798b3 100644
--- a/src/server/operandi_server/routers/workflow_utils.py
+++ b/src/server/operandi_server/routers/workflow_utils.py
@@ -62,10 +62,12 @@ async def nf_script_executable_steps_with_handling(logger, nf_script_path: str)
     try:
         with open(nf_script_path) as nf_file:
             line = nf_file.readline()
-            for word in line.split(' '):
-                if "ocrd-" in word:
-                    processor_executables.append(word)
-                    break
+            while line:
+                for word in line.split(' '):
+                    if "ocrd-" in word:
+                        processor_executables.append(word)
+                        break
+                line = nf_file.readline()
     except Exception as error:
         message = "Failed to identify processor executables in the provided Nextflow workflow."
         logger.error(f"{message}, error: {error}")
@@ -82,7 +84,7 @@ async def nf_script_executable_steps_with_handling(logger, nf_script_path: str)
         raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=message)
     return apptainer_images
     """
-
+    logger.info(f"Found processor executables: {processor_executables}")
     return processor_executables
 
 async def validate_oton_with_handling(logger, ocrd_process_txt_path: str):

From 24be118eed8e8243c55021595c72c41096b9a70a Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Fri, 29 Nov 2024 20:00:44 +0100
Subject: [PATCH 12/16] fix: slim containers solution

---
 .../batch_submit_workflow_job.sh              | 30 +++-----
 src/utils/operandi_utils/hpc/nhr_executor.py  | 71 ++++++++++++-------
 .../test_3_hpc/test_3_nhr_combined.py         |  2 +-
 3 files changed, 57 insertions(+), 46 deletions(-)

diff --git a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
index 8f807194..cc2dcafa 100755
--- a/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
+++ b/src/utils/operandi_utils/hpc/batch_scripts/batch_submit_workflow_job.sh
@@ -36,6 +36,7 @@ FILE_GROUPS_TO_REMOVE=$(echo "$json_args" | jq .file_groups_to_remove | tr -d '"
 WORKFLOW_JOB_DIR=$(echo "$json_args" | jq .hpc_workflow_job_dir | tr -d '"')
 WORKSPACE_DIR=$(echo "$json_args" | jq .hpc_workspace_dir | tr -d '"')
 NF_RUN_COMMAND=$(echo "$json_args" | jq .nf_run_command | tr -d '"')
+PRINT_OCRD_VERSION_COMMAND=$(echo "$json_args" | jq .print_ocrd_version_command | tr -d '"')
 START_METS_SERVER_COMMAND=$(echo "$json_args" | jq .start_mets_server_command | tr -d '"')
 STOP_METS_SERVER_COMMAND=$(echo "$json_args" | jq .stop_mets_server_command | tr -d '"')
 LIST_FILE_GROUPS_COMMAND=$(echo "$json_args" | jq .list_file_groups_command | tr -d '"')
@@ -43,19 +44,15 @@ REMOVE_FILE_GROUP_COMMAND=$(echo "$json_args" | jq .remove_file_group_command |
 
 PROJECT_DIR_OCRD_MODELS="${PROJECT_BASE_DIR}/ocrd_models"
 PROJECT_DIR_PROCESSOR_SIFS="${PROJECT_BASE_DIR}/ocrd_processor_sifs"
-PROJECT_SIF_PATH_OCRD_ALL="${PROJECT_BASE_DIR}/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
 
 NODE_DIR_OCRD_MODELS="${TMP_LOCAL}/ocrd_models"
 NODE_DIR_PROCESSOR_SIFS="${TMP_LOCAL}/ocrd_processor_sifs"
-NODE_SIF_PATH_OCRD_ALL="${TMP_LOCAL}/ocrd_processor_sifs/ocrd_all_maximum_image.sif"
 
 echo ""
 echo "Project dir ocrd models: $PROJECT_DIR_OCRD_MODELS"
 echo "Project dir processor sifs: $PROJECT_DIR_PROCESSOR_SIFS"
-echo "Project sif path ocrd all: $PROJECT_SIF_PATH_OCRD_ALL"
 echo "Node dir ocrd models: $NODE_DIR_OCRD_MODELS"
 echo "Node dir processor sifs: $NODE_DIR_PROCESSOR_SIFS"
-echo "Node sif path ocrd all: $NODE_SIF_PATH_OCRD_ALL"
 echo ""
 
 echo "Workspace dir: $WORKSPACE_DIR"
@@ -63,18 +60,19 @@ echo "Use mets server: $USE_METS_SERVER"
 
 echo ""
 echo "Nf run command with Node placeholders: $NF_RUN_COMMAND"
-NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
 NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_NODE_DIR_OCRD_MODELS/$NODE_DIR_OCRD_MODELS}"
 NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_CMD_WRAPPER/\'}"
+NF_RUN_COMMAND="${NF_RUN_COMMAND//PH_NODE_DIR_PROCESSOR_SIFS/$NODE_DIR_PROCESSOR_SIFS}"
 echo ""
 echo "Nf run command without placeholders: $NF_RUN_COMMAND"
 echo ""
 
-echo "Replacing ocrd core image sif placeholder of commands"
-START_METS_SERVER_COMMAND="${START_METS_SERVER_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
-STOP_METS_SERVER_COMMAND="${STOP_METS_SERVER_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
-LIST_FILE_GROUPS_COMMAND="${LIST_FILE_GROUPS_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
-REMOVE_FILE_GROUP_COMMAND="${REMOVE_FILE_GROUP_COMMAND//PH_NODE_SIF_PATH_OCRD_ALL/$NODE_SIF_PATH_OCRD_ALL}"
+echo "Replacing ocrd core NODE_DIR_PROCESSOR_SIFS"
+PRINT_OCRD_VERSION_COMMAND="${PRINT_OCRD_VERSION_COMMAND//PH_NODE_DIR_PROCESSOR_SIFS/$NODE_DIR_PROCESSOR_SIFS}"
+START_METS_SERVER_COMMAND="${START_METS_SERVER_COMMAND//PH_NODE_DIR_PROCESSOR_SIFS/$NODE_DIR_PROCESSOR_SIFS}"
+STOP_METS_SERVER_COMMAND="${STOP_METS_SERVER_COMMAND//PH_NODE_DIR_PROCESSOR_SIFS/$NODE_DIR_PROCESSOR_SIFS}"
+LIST_FILE_GROUPS_COMMAND="${LIST_FILE_GROUPS_COMMAND//PH_NODE_DIR_PROCESSOR_SIFS/$NODE_DIR_PROCESSOR_SIFS}"
+REMOVE_FILE_GROUP_COMMAND="${REMOVE_FILE_GROUP_COMMAND//PH_NODE_DIR_PROCESSOR_SIFS/$NODE_DIR_PROCESSOR_SIFS}"
 echo ""
 
 check_existence_of_dir_scratch_base(){
@@ -98,15 +96,6 @@ check_existence_of_dir_ocrd_models(){
   echo "Ocrd models directory found at: ${PROJECT_DIR_OCRD_MODELS}"
 }
 
-check_existence_of_sif_path_ocrd_all(){
-  # The SIF file of the OCR-D All docker image must be previously created
-  if [ ! -f "${PROJECT_SIF_PATH_OCRD_ALL}" ]; then
-    echo "Required ocrd_all_image sif file not found at: ${PROJECT_SIF_PATH_OCRD_ALL}"
-    exit 1
-  fi
-  echo "Required ocrd_all_image sif file found at: ${PROJECT_SIF_PATH_OCRD_ALL}"
-}
-
 check_existence_of_ocrd_processor_images_to_be_used(){
   for ocrd_image in "${ocrd_processor_images[@]}"
   do
@@ -121,7 +110,6 @@ check_existence_of_ocrd_processor_images_to_be_used(){
 check_existence_of_paths() {
   check_existence_of_dir_scratch_base
   check_existence_of_dir_ocrd_models
-  check_existence_of_sif_path_ocrd_all
   check_existence_of_ocrd_processor_images_to_be_used
 }
 
@@ -172,7 +160,7 @@ transfer_to_node_storage_processor_images(){
     fi
   done
   echo ""
-  apptainer exec "$NODE_SIF_PATH_OCRD_ALL" ocrd --version
+  eval "$PRINT_OCRD_VERSION_COMMAND"
   echo ""
 }
 
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index b278d1ef..c0b7d2fc 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -5,13 +5,18 @@
 from time import sleep
 from typing import List
 
-from operandi_utils.constants import StateJobSlurm
+from operandi_utils.constants import StateJobSlurm, OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE
 from .constants import (
     HPC_JOB_DEADLINE_TIME_TEST, HPC_JOB_QOS_DEFAULT, HPC_NHR_JOB_DEFAULT_PARTITION, HPC_BATCH_SUBMIT_WORKFLOW_JOB,
     HPC_WRAPPER_SUBMIT_WORKFLOW_JOB, HPC_WRAPPER_CHECK_WORKFLOW_JOB_STATUS
 )
 from .nhr_connector import NHRConnector
 
+# Just some placeholders to be replaced with actual paths that are
+# dynamically allocated inside the node that runs the HPC slurm job
+PH_NODE_DIR_OCRD_MODELS = "PH_NODE_DIR_OCRD_MODELS"
+PH_NODE_DIR_PROCESSOR_SIFS = "PH_NODE_DIR_PROCESSOR_SIFS"
+PH_CMD_WRAPPER = "PH_CMD_WRAPPER"
 
 class NHRExecutor(NHRConnector):
     def __init__(self) -> None:
@@ -67,23 +72,33 @@ def trigger_slurm_job(
         hpc_nf_script_path = join(self.slurm_workspaces_dir, workflow_job_id, nextflow_script_id)
         hpc_workspace_dir = join(self.slurm_workspaces_dir, workflow_job_id, workspace_id)
 
-        # NODE_PATH_OCRD_MODELS_PLACEHOLDER and NODE_PATH_SIF_PLACEHOLDER are just placeholders to be replaced
-        # with actual paths that are dynamically allocated inside the node that runs the HPC slurm job
-        ph_node_dir_ocrd_models = "PH_NODE_DIR_OCRD_MODELS"
-        ph_node_sif_path_ocrd_all = "PH_NODE_SIF_PATH_OCRD_ALL"
+        sif_ocrd_all = "ocrd_all_maximum_image.sif"
+        sif_ocrd_core = OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE["ocrd"]
 
+        # TODO: Refactor the switch for using slim images
+        use_slim_images = False
+        if use_slim_images:
+            ph_sif_core = f"{PH_NODE_DIR_PROCESSOR_SIFS}/{sif_ocrd_core}"
+        else:
+            ph_sif_core = f"{PH_NODE_DIR_PROCESSOR_SIFS}/{sif_ocrd_all}"
         nf_run_command = self.cmd_nextflow_run(
             hpc_nf_script_path=hpc_nf_script_path, hpc_ws_dir=hpc_workspace_dir,
-            bind_ocrd_models=f"{ph_node_dir_ocrd_models}/ocrd-resources:/usr/local/share/ocrd-resources",
-            ph_sif_ocrd_all=ph_node_sif_path_ocrd_all, input_file_grp=input_file_grp, mets_basename=mets_basename,
+            bind_ocrd_models=f"{PH_NODE_DIR_OCRD_MODELS}/ocrd-resources:/usr/local/share/ocrd-resources",
+            sif_core=sif_ocrd_core,
+            sif_ocrd_all=sif_ocrd_all, input_file_grp=input_file_grp, mets_basename=mets_basename,
             use_mets_server=use_mets_server, nf_executable_steps=nf_executable_steps, ws_pages_amount=ws_pages_amount,
-            cpus=cpus, ram=ram, forks=nf_process_forks
+            cpus=cpus, ram=ram, forks=nf_process_forks, use_slim_images=use_slim_images
         )
 
+        if use_slim_images:
+            ocrd_processor_images = ",".join([OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE[exe] for exe in nf_executable_steps])
+            ocrd_processor_images = f"{sif_ocrd_core},{ocrd_processor_images}"
+        else:
+            ocrd_processor_images = sif_ocrd_all
         regular_args = {
             "project_base_dir": self.project_root_dir,
             "scratch_base_dir": self.slurm_workspaces_dir,
-            "ocrd_processor_images": "ocrd_all_maximum_image.sif",
+            "ocrd_processor_images": ocrd_processor_images,
             "workflow_job_id": workflow_job_id,
             "workspace_id": workspace_id,
             "use_mets_server_bash_flag": use_mets_server_bash_flag,
@@ -91,10 +106,11 @@ def trigger_slurm_job(
             "hpc_workflow_job_dir": hpc_workflow_job_dir,
             "hpc_workspace_dir": hpc_workspace_dir,
             "nf_run_command": nf_run_command,
-            "start_mets_server_command": self.cmd_core_start_mets_server(hpc_workspace_dir, ph_node_sif_path_ocrd_all),
-            "stop_mets_server_command": self.cmd_core_stop_mets_server(hpc_workspace_dir, ph_node_sif_path_ocrd_all),
-            "list_file_groups_command": self.cmd_core_list_file_groups(hpc_workspace_dir, ph_node_sif_path_ocrd_all),
-            "remove_file_group_command": self.cmd_core_remove_file_group(hpc_workspace_dir, ph_node_sif_path_ocrd_all)
+            "print_ocrd_version_command": self.cmd_core_print_version(hpc_workspace_dir, ph_sif_core),
+            "start_mets_server_command": self.cmd_core_start_mets_server(hpc_workspace_dir, ph_sif_core),
+            "stop_mets_server_command": self.cmd_core_stop_mets_server(hpc_workspace_dir, ph_sif_core),
+            "list_file_groups_command": self.cmd_core_list_file_groups(hpc_workspace_dir, ph_sif_core),
+            "remove_file_group_command": self.cmd_core_remove_file_group(hpc_workspace_dir, ph_sif_core)
         }
         command += f" '{dumps(sbatch_args)}' '{dumps(regular_args)}'"
 
@@ -176,9 +192,9 @@ def poll_till_end_slurm_job_state(self, slurm_job_id: str, interval: int = 5, ti
 
     @staticmethod
     def cmd_nextflow_run(
-        hpc_nf_script_path: str, hpc_ws_dir: str, bind_ocrd_models: str, ph_sif_ocrd_all: str, input_file_grp: str,
-        mets_basename: str, use_mets_server: bool, nf_executable_steps: List[str], ws_pages_amount: int, cpus: int,
-        ram: int, forks: int
+        hpc_nf_script_path: str, hpc_ws_dir: str, bind_ocrd_models: str, sif_core: str, sif_ocrd_all: str,
+        input_file_grp: str, mets_basename: str, use_mets_server: bool, nf_executable_steps: List[str],
+        ws_pages_amount: int, cpus: int, ram: int, forks: int, use_slim_images: bool
     ) -> str:
         nf_run_command = f"nextflow run {hpc_nf_script_path} -ansi-log false -with-report"
         nf_run_command += f" --input_file_group {input_file_grp}"
@@ -187,22 +203,29 @@ def cmd_nextflow_run(
             nf_run_command += f" --mets_socket /ws_data/mets_server.sock"
         nf_run_command += f" --workspace_dir /ws_data"
         nf_run_command += f" --pages {ws_pages_amount}"
-        # Command wrapper placeholder. Each occurrence is replaced with a single quote ' to avoid json parsing errors
 
-        # TODO: Send actual slim image apptainer cmds here instead of the sif_ocrd_all
-        ph_cmd_wrapper = "PH_CMD_WRAPPER"
-        index = 0
+        sif_images = [OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE[exe] for exe in nf_executable_steps]
         apptainer_cmd = f"apptainer exec --bind {hpc_ws_dir}:/ws_data --bind {bind_ocrd_models}"
-        apptainer_cmd += f" --env OCRD_METS_CACHING=false {ph_sif_ocrd_all}"
-        nf_run_command += f" --env_wrapper_cmd_core {ph_cmd_wrapper}{apptainer_cmd}{ph_cmd_wrapper}"
-        for executable_step in nf_executable_steps:
-            nf_run_command += f" --env_wrapper_cmd_step{index} {ph_cmd_wrapper}{apptainer_cmd}{ph_cmd_wrapper}"
+        apptainer_cmd += f" --env OCRD_METS_CACHING=false"
+        apptainer_image = sif_core if use_slim_images else sif_ocrd_all
+        core_command = f"{apptainer_cmd} {PH_NODE_DIR_PROCESSOR_SIFS}/{apptainer_image}"
+        nf_run_command += f" --env_wrapper_cmd_core {PH_CMD_WRAPPER}{core_command}{PH_CMD_WRAPPER}"
+
+        index = 0
+        for sif_image in sif_images:
+            apptainer_image = sif_image if use_slim_images else sif_ocrd_all
+            step_command = f"{apptainer_cmd} {PH_NODE_DIR_PROCESSOR_SIFS}/{apptainer_image}"
+            nf_run_command += f" --env_wrapper_cmd_step{index} {PH_CMD_WRAPPER}{step_command}{PH_CMD_WRAPPER}"
             index += 1
         nf_run_command += f" --cpus {cpus}"
         nf_run_command += f" --ram {ram}"
         nf_run_command += f" --forks {forks}"
         return nf_run_command
 
+    @staticmethod
+    def cmd_core_print_version(hpc_ws_dir: str, ph_sif_core: str) -> str:
+        return f"apptainer exec --bind {hpc_ws_dir}:/ws_data {ph_sif_core} ocrd --version"
+
     @staticmethod
     def cmd_core_start_mets_server(hpc_ws_dir: str, ph_sif_core: str) -> str:
         command = f"apptainer exec --bind {hpc_ws_dir}:/ws_data {ph_sif_core}"
diff --git a/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
index c584386d..13c772e1 100644
--- a/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
+++ b/tests/tests_utils/test_3_hpc/test_3_nhr_combined.py
@@ -56,7 +56,7 @@ def test_pack_and_put_slurm_workspace_with_ms(
     )
 
 
-def _test_hpc_connector_run_batch_script(
+def test_hpc_connector_run_batch_script(
     hpc_nhr_command_executor, hpc_nhr_data_transfer, template_workflow):
     slurm_job_id = hpc_nhr_command_executor.trigger_slurm_job(
         workflow_job_id=ID_WORKFLOW_JOB, nextflow_script_path=Path(template_workflow),

From 3a20a9a6f517158cbb97cab4ea6ff21626673256 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Mon, 2 Dec 2024 14:02:55 +0100
Subject: [PATCH 13/16] refactor: slim images switch

---
 src/utils/operandi_utils/hpc/constants.py    |  4 ++++
 src/utils/operandi_utils/hpc/nhr_executor.py | 10 ++++------
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/utils/operandi_utils/hpc/constants.py b/src/utils/operandi_utils/hpc/constants.py
index 156cd45a..5ce9f88c 100644
--- a/src/utils/operandi_utils/hpc/constants.py
+++ b/src/utils/operandi_utils/hpc/constants.py
@@ -13,6 +13,7 @@
     "HPC_SSH_CONNECTION_TRY_TIMES",
     "HPC_NHR_PROJECT",
     "HPC_NHR_CLUSTERS",
+    "HPC_USE_SLIM_IMAGES",
     "HPC_WRAPPER_SUBMIT_WORKFLOW_JOB",
     "HPC_WRAPPER_CHECK_WORKFLOW_JOB_STATUS"
 ]
@@ -78,3 +79,6 @@
 HPC_JOB_QOS_LONG = "7d"
 HPC_JOB_QOS_VERY_LONG = "14d"
 HPC_SSH_CONNECTION_TRY_TIMES = 30
+
+# A switch to decide whether to use the fat ocrd_all image or slim images of the processors
+HPC_USE_SLIM_IMAGES: bool = False
diff --git a/src/utils/operandi_utils/hpc/nhr_executor.py b/src/utils/operandi_utils/hpc/nhr_executor.py
index c0b7d2fc..36a48acc 100644
--- a/src/utils/operandi_utils/hpc/nhr_executor.py
+++ b/src/utils/operandi_utils/hpc/nhr_executor.py
@@ -8,7 +8,7 @@
 from operandi_utils.constants import StateJobSlurm, OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE
 from .constants import (
     HPC_JOB_DEADLINE_TIME_TEST, HPC_JOB_QOS_DEFAULT, HPC_NHR_JOB_DEFAULT_PARTITION, HPC_BATCH_SUBMIT_WORKFLOW_JOB,
-    HPC_WRAPPER_SUBMIT_WORKFLOW_JOB, HPC_WRAPPER_CHECK_WORKFLOW_JOB_STATUS
+    HPC_USE_SLIM_IMAGES, HPC_WRAPPER_SUBMIT_WORKFLOW_JOB, HPC_WRAPPER_CHECK_WORKFLOW_JOB_STATUS
 )
 from .nhr_connector import NHRConnector
 
@@ -75,9 +75,7 @@ def trigger_slurm_job(
         sif_ocrd_all = "ocrd_all_maximum_image.sif"
         sif_ocrd_core = OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE["ocrd"]
 
-        # TODO: Refactor the switch for using slim images
-        use_slim_images = False
-        if use_slim_images:
+        if HPC_USE_SLIM_IMAGES:
             ph_sif_core = f"{PH_NODE_DIR_PROCESSOR_SIFS}/{sif_ocrd_core}"
         else:
             ph_sif_core = f"{PH_NODE_DIR_PROCESSOR_SIFS}/{sif_ocrd_all}"
@@ -87,10 +85,10 @@ def trigger_slurm_job(
             sif_core=sif_ocrd_core,
             sif_ocrd_all=sif_ocrd_all, input_file_grp=input_file_grp, mets_basename=mets_basename,
             use_mets_server=use_mets_server, nf_executable_steps=nf_executable_steps, ws_pages_amount=ws_pages_amount,
-            cpus=cpus, ram=ram, forks=nf_process_forks, use_slim_images=use_slim_images
+            cpus=cpus, ram=ram, forks=nf_process_forks, use_slim_images=HPC_USE_SLIM_IMAGES
         )
 
-        if use_slim_images:
+        if HPC_USE_SLIM_IMAGES:
             ocrd_processor_images = ",".join([OCRD_PROCESSOR_EXECUTABLE_TO_IMAGE[exe] for exe in nf_executable_steps])
             ocrd_processor_images = f"{sif_ocrd_core},{ocrd_processor_images}"
         else:

From 5177e1282e8523f3cead173bf628bcf6e9452208 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Mon, 2 Dec 2024 15:21:49 +0100
Subject: [PATCH 14/16] add: info print on oton produced wfs

---
 .../nextflow_workflows/default_workflow.nf    | 23 ++++++++++++++++
 .../default_workflow_with_MS.nf               | 24 +++++++++++++++++
 .../hpc/nextflow_workflows/odem_workflow.nf   | 25 ++++++++++++++++++
 .../odem_workflow_with_MS.nf                  | 26 +++++++++++++++++++
 .../hpc/nextflow_workflows/sbb_workflow.nf    | 16 ++++++++++++
 .../sbb_workflow_with_MS.nf                   | 17 ++++++++++++
 .../nextflow_workflows/template_workflow.nf   | 16 ++++++++++++
 .../template_workflow_with_MS.nf              | 17 ++++++++++++
 .../operandi_utils/oton/nf_file_executable.py | 15 +++++++++++
 .../oton/test_output_nextflow1_apptainer.nf   | 23 ++++++++++++++++
 ...test_output_nextflow1_apptainer_with_MS.nf | 24 +++++++++++++++++
 .../oton/test_output_nextflow1_docker.nf      | 19 ++++++++++++++
 .../test_output_nextflow1_docker_with_MS.nf   | 20 ++++++++++++++
 .../oton/test_output_nextflow1_local.nf       | 18 +++++++++++++
 .../test_output_nextflow1_local_with_MS.nf    | 19 ++++++++++++++
 tests/assets/oton/test_output_nextflow2.nf    | 17 ++++++++++++
 tests/assets/oton/test_output_nextflow3.nf    | 13 ++++++++++
 tests/assets/oton/test_output_nextflow4.nf    | 23 ++++++++++++++++
 18 files changed, 355 insertions(+)

diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
index b057341e..a748cf8b 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
@@ -20,6 +20,29 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
index 590ba3c4..23115cd0 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
@@ -21,6 +21,30 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
index 78c6f2c2..8d3908c2 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
@@ -22,6 +22,31 @@ params.env_wrapper_cmd_step7 = "null"
 params.env_wrapper_cmd_step8 = "null"
 params.env_wrapper_cmd_step9 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    env_wrapper_cmd_step8: ${params.env_wrapper_cmd_step8}
+    env_wrapper_cmd_step9: ${params.env_wrapper_cmd_step9}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
index 240ae719..63fe0753 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
@@ -23,6 +23,32 @@ params.env_wrapper_cmd_step7 = "null"
 params.env_wrapper_cmd_step8 = "null"
 params.env_wrapper_cmd_step9 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    env_wrapper_cmd_step8: ${params.env_wrapper_cmd_step8}
+    env_wrapper_cmd_step9: ${params.env_wrapper_cmd_step9}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf
index b7d3a235..eb37866b 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow.nf
@@ -13,6 +13,22 @@ params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toI
 params.env_wrapper_cmd_core = "null"
 params.env_wrapper_cmd_step0 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf
index 389772b5..e81b6094 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/sbb_workflow_with_MS.nf
@@ -14,6 +14,23 @@ params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toI
 params.env_wrapper_cmd_core = "null"
 params.env_wrapper_cmd_step0 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf
index fc01fceb..0028a978 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow.nf
@@ -13,6 +13,22 @@ params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toI
 params.env_wrapper_cmd_core = "null"
 params.env_wrapper_cmd_step0 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf
index be041784..0daa30ed 100755
--- a/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf
+++ b/src/utils/operandi_utils/hpc/nextflow_workflows/template_workflow_with_MS.nf
@@ -14,6 +14,23 @@ params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toI
 params.env_wrapper_cmd_core = "null"
 params.env_wrapper_cmd_step0 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/src/utils/operandi_utils/oton/nf_file_executable.py b/src/utils/operandi_utils/oton/nf_file_executable.py
index ef6b7529..61cf247e 100644
--- a/src/utils/operandi_utils/oton/nf_file_executable.py
+++ b/src/utils/operandi_utils/oton/nf_file_executable.py
@@ -193,6 +193,19 @@ def __assign_first_file_grps_param(self):
                 break
             index += 1
 
+    def build_log_info_prints(self) -> str:
+        log_info = f'log.info """\\\n'
+        log_info += f"{SPACES}OPERANDI HPC - Nextflow Workflow\n"
+        log_info += f"{SPACES}===================================================\n"
+        for param in self.nf_lines_parameters:
+            if not param or "params." not in param:
+                continue
+            param_key = param[param.find(".") + 1:param.find("=") - 1]
+            log_info += f"{SPACES}{param_key}: "
+            log_info += f'${BS[0]}{param[0:param.find("=") - 1]}{BS[1]}\n'
+        log_info += f'{SPACES}""".stripIndent()\n'
+        return log_info
+
     # TODO: Refactor later
     def build_main_workflow(self, with_mets_server: bool):
         self.__assign_first_file_grps_param()
@@ -213,6 +226,8 @@ def produce_nextflow_file(self, output_path: str, environment: str, with_mets_se
             for nextflow_line in self.nf_lines_parameters:
                 nextflow_file.write(f'{nextflow_line}\n')
             nextflow_file.write("\n")
+            nextflow_file.write(self.build_log_info_prints())
+            nextflow_file.write("\n")
             nextflow_file.write(f'{self.nf_process_split_range.file_representation(local_script=True)}\n')
             for block in self.nf_blocks_process:
                 nextflow_file.write(f'{block.file_representation(local_script=False)}\n')
diff --git a/tests/assets/oton/test_output_nextflow1_apptainer.nf b/tests/assets/oton/test_output_nextflow1_apptainer.nf
index b057341e..a748cf8b 100644
--- a/tests/assets/oton/test_output_nextflow1_apptainer.nf
+++ b/tests/assets/oton/test_output_nextflow1_apptainer.nf
@@ -20,6 +20,29 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf b/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
index 590ba3c4..23115cd0 100644
--- a/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_apptainer_with_MS.nf
@@ -21,6 +21,30 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    cpus: ${params.cpus}
+    ram: ${params.ram}
+    forks: ${params.forks}
+    cpus_per_fork: ${params.cpus_per_fork}
+    ram_per_fork: ${params.ram_per_fork}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow1_docker.nf b/tests/assets/oton/test_output_nextflow1_docker.nf
index 4f59235a..638e6190 100644
--- a/tests/assets/oton/test_output_nextflow1_docker.nf
+++ b/tests/assets/oton/test_output_nextflow1_docker.nf
@@ -16,6 +16,25 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    forks: ${params.forks}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf b/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
index 105bd787..e702bba1 100644
--- a/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_docker_with_MS.nf
@@ -17,6 +17,26 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    forks: ${params.forks}
+    env_wrapper_cmd_core: ${params.env_wrapper_cmd_core}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow1_local.nf b/tests/assets/oton/test_output_nextflow1_local.nf
index 812258c8..0aad272f 100644
--- a/tests/assets/oton/test_output_nextflow1_local.nf
+++ b/tests/assets/oton/test_output_nextflow1_local.nf
@@ -15,6 +15,24 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    forks: ${params.forks}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow1_local_with_MS.nf b/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
index 7685e74c..58ed1547 100644
--- a/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
+++ b/tests/assets/oton/test_output_nextflow1_local_with_MS.nf
@@ -16,6 +16,25 @@ params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 params.env_wrapper_cmd_step7 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    mets_socket_path: ${params.mets_socket_path}
+    forks: ${params.forks}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow2.nf b/tests/assets/oton/test_output_nextflow2.nf
index a10ca1ad..f6eaf54a 100644
--- a/tests/assets/oton/test_output_nextflow2.nf
+++ b/tests/assets/oton/test_output_nextflow2.nf
@@ -14,6 +14,23 @@ params.env_wrapper_cmd_step4 = "null"
 params.env_wrapper_cmd_step5 = "null"
 params.env_wrapper_cmd_step6 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    forks: ${params.forks}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow3.nf b/tests/assets/oton/test_output_nextflow3.nf
index 4e551f1e..aba90b96 100644
--- a/tests/assets/oton/test_output_nextflow3.nf
+++ b/tests/assets/oton/test_output_nextflow3.nf
@@ -10,6 +10,19 @@ params.env_wrapper_cmd_step0 = "null"
 params.env_wrapper_cmd_step1 = "null"
 params.env_wrapper_cmd_step2 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    forks: ${params.forks}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks
diff --git a/tests/assets/oton/test_output_nextflow4.nf b/tests/assets/oton/test_output_nextflow4.nf
index 1d4f600b..0f8bb59c 100644
--- a/tests/assets/oton/test_output_nextflow4.nf
+++ b/tests/assets/oton/test_output_nextflow4.nf
@@ -20,6 +20,29 @@ params.env_wrapper_cmd_step10 = "null"
 params.env_wrapper_cmd_step11 = "null"
 params.env_wrapper_cmd_step12 = "null"
 
+log.info """\
+    OPERANDI HPC - Nextflow Workflow
+    ===================================================
+    input_file_group: ${params.input_file_group}
+    mets_path: ${params.mets_path}
+    workspace_dir: ${params.workspace_dir}
+    pages: ${params.pages}
+    forks: ${params.forks}
+    env_wrapper_cmd_step0: ${params.env_wrapper_cmd_step0}
+    env_wrapper_cmd_step1: ${params.env_wrapper_cmd_step1}
+    env_wrapper_cmd_step2: ${params.env_wrapper_cmd_step2}
+    env_wrapper_cmd_step3: ${params.env_wrapper_cmd_step3}
+    env_wrapper_cmd_step4: ${params.env_wrapper_cmd_step4}
+    env_wrapper_cmd_step5: ${params.env_wrapper_cmd_step5}
+    env_wrapper_cmd_step6: ${params.env_wrapper_cmd_step6}
+    env_wrapper_cmd_step7: ${params.env_wrapper_cmd_step7}
+    env_wrapper_cmd_step8: ${params.env_wrapper_cmd_step8}
+    env_wrapper_cmd_step9: ${params.env_wrapper_cmd_step9}
+    env_wrapper_cmd_step10: ${params.env_wrapper_cmd_step10}
+    env_wrapper_cmd_step11: ${params.env_wrapper_cmd_step11}
+    env_wrapper_cmd_step12: ${params.env_wrapper_cmd_step12}
+    """.stripIndent()
+
 process split_page_ranges {
     debug true
     maxForks params.forks

From 172474d1bca055eab41c419e06bbae8320626896 Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Mon, 2 Dec 2024 16:17:32 +0100
Subject: [PATCH 15/16] used dict for nf_params

---
 src/utils/operandi_utils/oton/constants.py    | 13 ---
 .../operandi_utils/oton/nf_file_executable.py | 79 +++++++------------
 tests/assets/oton/constants.py                | 53 ++++++-------
 tests/tests_utils/test_2_oton/assert_utils.py |  2 +-
 .../test_2_oton/test_3_converter_1_local.py   | 10 +--
 5 files changed, 62 insertions(+), 95 deletions(-)

diff --git a/src/utils/operandi_utils/oton/constants.py b/src/utils/operandi_utils/oton/constants.py
index 80750029..180fc94b 100644
--- a/src/utils/operandi_utils/oton/constants.py
+++ b/src/utils/operandi_utils/oton/constants.py
@@ -32,17 +32,4 @@
 PARAMS_KEY_CPUS_PER_FORK: str = 'params.cpus_per_fork'
 PARAMS_KEY_RAM_PER_FORK: str = 'params.ram_per_fork'
 
-REPR_INPUT_FILE_GRP: str = f"""{PARAMS_KEY_INPUT_FILE_GRP} = "null\""""
-REPR_METS_PATH: str = f"""{PARAMS_KEY_METS_PATH} = "null\""""
-REPR_METS_SOCKET_PATH: str = f"""{PARAMS_KEY_METS_SOCKET_PATH} = "null\""""
-REPR_WORKSPACE_DIR: str = f"""{PARAMS_KEY_WORKSPACE_DIR} = "null\""""
-REPR_ENV_WRAPPER_CMD_CORE: str = f"""{PARAMS_KEY_ENV_WRAPPER_CMD_CORE} = "null\""""
-REPR_PAGES: str = f"""{PARAMS_KEY_PAGES} = "null\""""
-REPR_CPUS: str = f"""{PARAMS_KEY_CPUS} = "null\""""
-REPR_RAM: str = f"""{PARAMS_KEY_RAM} = "null\""""
-REPR_FORKS: str = f"""{PARAMS_KEY_FORKS} = {PARAMS_KEY_CPUS}"""
-REPR_FORKS_NULL: str = f"""{PARAMS_KEY_FORKS} = "4\""""
-REPR_CPUS_PER_FORK: str = f"""{PARAMS_KEY_CPUS_PER_FORK} = ({PARAMS_KEY_CPUS}.toInteger() / {PARAMS_KEY_FORKS}.toInteger()).intValue()"""
-REPR_RAM_PER_FORK: str = f"""{PARAMS_KEY_RAM_PER_FORK} = sprintf("%dGB", ({PARAMS_KEY_RAM}.toInteger() / {PARAMS_KEY_FORKS}.toInteger()).intValue())"""
-
 WORKFLOW_COMMENT = f"// This workflow was automatically generated by the v{OPERANDI_VERSION} operandi_utils.oton module"
diff --git a/src/utils/operandi_utils/oton/nf_file_executable.py b/src/utils/operandi_utils/oton/nf_file_executable.py
index 61cf247e..57d8d31c 100644
--- a/src/utils/operandi_utils/oton/nf_file_executable.py
+++ b/src/utils/operandi_utils/oton/nf_file_executable.py
@@ -11,20 +11,12 @@
     PARAMS_KEY_ENV_WRAPPER_CMD_CORE,
     PARAMS_KEY_ENV_WRAPPER_CMD_STEP,
     PARAMS_KEY_FORKS,
+    PARAMS_KEY_PAGES,
+    PARAMS_KEY_CPUS,
     PARAMS_KEY_CPUS_PER_FORK,
+    PARAMS_KEY_RAM,
     PARAMS_KEY_RAM_PER_FORK,
-    REPR_ENV_WRAPPER_CMD_CORE,
-    REPR_INPUT_FILE_GRP,
-    REPR_METS_PATH,
-    REPR_METS_SOCKET_PATH,
-    REPR_WORKSPACE_DIR,
-    REPR_PAGES,
-    REPR_CPUS,
-    REPR_RAM,
-    REPR_FORKS,
-    REPR_FORKS_NULL,
-    REPR_CPUS_PER_FORK,
-    REPR_RAM_PER_FORK,
+    PARAMS_KEY_METS_SOCKET_PATH,
     SPACES,
     WORKFLOW_COMMENT
 )
@@ -38,7 +30,7 @@ def __init__(self):
         self.logger.setLevel(getLevelName(OTON_LOG_LEVEL))
 
         self.supported_environments = ["local", "docker", "apptainer"]
-        self.nf_lines_parameters: List[str] = []
+        self.nf_lines_parameters = {}
         self.nf_process_split_range = None
         self.nf_process_merging_mets = None
         self.nf_blocks_process: List[NextflowBlockProcess] = []
@@ -48,28 +40,28 @@ def build_parameters(self, environment: str, with_mets_server: bool):
         if environment not in self.supported_environments:
             raise ValueError(f"Invalid environment value: {environment}. Must be one of: {self.supported_environments}")
 
-        self.nf_lines_parameters.append('nextflow.enable.dsl = 2')
-        self.nf_lines_parameters.append('')
-        self.nf_lines_parameters.append(REPR_INPUT_FILE_GRP)
-        self.nf_lines_parameters.append(REPR_METS_PATH)
-        self.nf_lines_parameters.append(REPR_WORKSPACE_DIR)
-        self.nf_lines_parameters.append(REPR_PAGES)
+        self.nf_lines_parameters[PARAMS_KEY_INPUT_FILE_GRP] = '"null"'
+        self.nf_lines_parameters[PARAMS_KEY_METS_PATH] = '"null"'
+        self.nf_lines_parameters[PARAMS_KEY_WORKSPACE_DIR] = '"null"'
+        self.nf_lines_parameters[PARAMS_KEY_PAGES] = '"null"'
 
         if with_mets_server:
-            self.nf_lines_parameters.append(REPR_METS_SOCKET_PATH)
+            self.nf_lines_parameters[PARAMS_KEY_METS_SOCKET_PATH] = '"null"'
 
         if environment == "local":
-            self.nf_lines_parameters.append(REPR_FORKS_NULL)
+            self.nf_lines_parameters[PARAMS_KEY_FORKS] = '"4"'
         if environment == "docker":
-            self.nf_lines_parameters.append(REPR_FORKS_NULL)
-            self.nf_lines_parameters.append(REPR_ENV_WRAPPER_CMD_CORE)
+            self.nf_lines_parameters[PARAMS_KEY_FORKS] = '"4"'
+            self.nf_lines_parameters[PARAMS_KEY_ENV_WRAPPER_CMD_CORE] = '"null"'
         if environment == "apptainer":
-            self.nf_lines_parameters.append(REPR_CPUS)
-            self.nf_lines_parameters.append(REPR_RAM)
-            self.nf_lines_parameters.append(REPR_FORKS)
-            self.nf_lines_parameters.append(REPR_CPUS_PER_FORK)
-            self.nf_lines_parameters.append(REPR_RAM_PER_FORK)
-            self.nf_lines_parameters.append(REPR_ENV_WRAPPER_CMD_CORE)
+            self.nf_lines_parameters[PARAMS_KEY_CPUS] = '"null"'
+            self.nf_lines_parameters[PARAMS_KEY_RAM] = '"null"'
+            self.nf_lines_parameters[PARAMS_KEY_FORKS] = f'{PARAMS_KEY_CPUS}'
+            self.nf_lines_parameters[PARAMS_KEY_CPUS_PER_FORK] = \
+                f'({PARAMS_KEY_CPUS}.toInteger() / {PARAMS_KEY_FORKS}.toInteger()).intValue()'
+            self.nf_lines_parameters[PARAMS_KEY_RAM_PER_FORK] = \
+                f'sprintf("%dGB", ({PARAMS_KEY_RAM}.toInteger() / {PARAMS_KEY_FORKS}.toInteger()).intValue())'
+            self.nf_lines_parameters[PARAMS_KEY_ENV_WRAPPER_CMD_CORE] = '"null"'
 
     # TODO: Refactor later
     def build_split_page_ranges_process(self, environment: str, with_mets_server: bool) -> NextflowBlockProcess:
@@ -180,35 +172,22 @@ def build_nextflow_processes(
             nf_process_block.add_parameter_output(parameter=CONST_METS_PATH, parameter_type='val')
             nf_process_block.add_parameter_output(parameter=CONST_PAGE_RANGE, parameter_type='val')
             nf_process_block.add_parameter_output(parameter=CONST_WORKSPACE_DIR, parameter_type='val')
-            self.nf_lines_parameters.append(f'{PARAMS_KEY_ENV_WRAPPER_CMD_STEP}{index} = "null"')
+            self.nf_lines_parameters[f'{PARAMS_KEY_ENV_WRAPPER_CMD_STEP}{index}'] = '"null"'
             self.nf_blocks_process.append(nf_process_block)
             index += 1
 
-    def __assign_first_file_grps_param(self):
-        first_file_grps = self.nf_blocks_process[0].processor_call_arguments.input_file_grps
-        index = 0
-        for parameter in self.nf_lines_parameters:
-            if PARAMS_KEY_INPUT_FILE_GRP in parameter:
-                self.nf_lines_parameters[index] = parameter.replace("null", first_file_grps)
-                break
-            index += 1
-
     def build_log_info_prints(self) -> str:
         log_info = f'log.info """\\\n'
         log_info += f"{SPACES}OPERANDI HPC - Nextflow Workflow\n"
         log_info += f"{SPACES}===================================================\n"
-        for param in self.nf_lines_parameters:
-            if not param or "params." not in param:
-                continue
-            param_key = param[param.find(".") + 1:param.find("=") - 1]
-            log_info += f"{SPACES}{param_key}: "
-            log_info += f'${BS[0]}{param[0:param.find("=") - 1]}{BS[1]}\n'
+        for key, value in self.nf_lines_parameters.items():
+            log_info += f"{SPACES}{key[len('params.'):]}: ${BS[0]}{key}{BS[1]}\n"
         log_info += f'{SPACES}""".stripIndent()\n'
         return log_info
 
-    # TODO: Refactor later
     def build_main_workflow(self, with_mets_server: bool):
-        self.__assign_first_file_grps_param()
+        first_file_grps = self.nf_blocks_process[0].processor_call_arguments.input_file_grps
+        self.nf_lines_parameters[PARAMS_KEY_INPUT_FILE_GRP] = f'"{first_file_grps}"'
         nf_workflow_block = NextflowBlockWorkflow(
             workflow_name="main",
             nf_processes=self.nf_blocks_process,
@@ -223,8 +202,10 @@ def produce_nextflow_file(self, output_path: str, environment: str, with_mets_se
         # Write Nextflow line tokens to an output file
         with open(output_path, mode='w', encoding='utf-8') as nextflow_file:
             nextflow_file.write(f"{WORKFLOW_COMMENT}\n")
-            for nextflow_line in self.nf_lines_parameters:
-                nextflow_file.write(f'{nextflow_line}\n')
+            nextflow_file.write("nextflow.enable.dsl = 2\n")
+            nextflow_file.write("\n")
+            for key, value in self.nf_lines_parameters.items():
+                nextflow_file.write(f'{key} = {value}\n')
             nextflow_file.write("\n")
             nextflow_file.write(self.build_log_info_prints())
             nextflow_file.write("\n")
diff --git a/tests/assets/oton/constants.py b/tests/assets/oton/constants.py
index b8f3e053..6e540e84 100644
--- a/tests/assets/oton/constants.py
+++ b/tests/assets/oton/constants.py
@@ -105,33 +105,32 @@
 }
 """
 
-PARAMETERS_COMMON = [
-    'nextflow.enable.dsl = 2',
-    'params.mets_path = "null"',
-    'params.workspace_dir = "null"',
-    'params.pages = "null"',
-]
+PARAMETERS_COMMON = {
+    'params.mets_path': '"null"',
+    'params.workspace_dir': '"null"',
+    'params.pages': '"null"',
+}
 
-PARAMETERS_LOCAL = [
-    'params.forks = "4"'
-]
+PARAMETERS_LOCAL = {
+    'params.forks': '"4"',
+}
 
-PARAMETERS_DOCKER = [
-    'params.forks = "4"',
-    'params.env_wrapper_cmd_core = "null"',
-    'params.env_wrapper_cmd_step0 = "null"',
-    'params.env_wrapper_cmd_step1 = "null"',
-    'params.env_wrapper_cmd_step2 = "null"',
-]
+PARAMETERS_DOCKER = {
+    'params.forks': '"4"',
+    'params.env_wrapper_cmd_core': '"null"',
+    'params.env_wrapper_cmd_step0': '"null"',
+    'params.env_wrapper_cmd_step1': '"null"',
+    'params.env_wrapper_cmd_step2': '"null"',
+}
 
-PARAMETERS_APPTAINER = [
-    'params.cpus = "null"',
-    'params.ram = "null"',
-    'params.forks = params.cpus',
-    'params.cpus_per_fork = (params.cpus.toInteger() / params.forks.toInteger()).intValue()',
-    'params.ram_per_fork = sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())',
-    'params.env_wrapper_cmd_core = "null"',
-    'params.env_wrapper_cmd_step0 = "null"',
-    'params.env_wrapper_cmd_step1 = "null"',
-    'params.env_wrapper_cmd_step2 = "null"',
-]
+PARAMETERS_APPTAINER = {
+    'params.cpus': '"null"',
+    'params.ram': '"null"',
+    'params.forks': 'params.cpus',
+    'params.cpus_per_fork': '(params.cpus.toInteger() / params.forks.toInteger()).intValue()',
+    'params.ram_per_fork': 'sprintf("%dGB", (params.ram.toInteger() / params.forks.toInteger()).intValue())',
+    'params.env_wrapper_cmd_core': '"null"',
+    'params.env_wrapper_cmd_step0': '"null"',
+    'params.env_wrapper_cmd_step1': '"null"',
+    'params.env_wrapper_cmd_step2': '"null"',
+}
diff --git a/tests/tests_utils/test_2_oton/assert_utils.py b/tests/tests_utils/test_2_oton/assert_utils.py
index ed197bea..11d334b7 100644
--- a/tests/tests_utils/test_2_oton/assert_utils.py
+++ b/tests/tests_utils/test_2_oton/assert_utils.py
@@ -13,7 +13,7 @@ def assert_common_features(
     for parameter in PARAMETERS_COMMON:
         assert parameter in parameters
     if with_mets_server:
-        assert 'params.mets_socket_path = "null"' in parameters, f"params.mets_socket_path is missing in {parameters}"
+        assert parameters['params.mets_socket_path'] == '"null"', f"params.mets_socket_path is missing in {parameters}"
     blocks_process = nextflow_file_class.nf_blocks_process
     assert len(blocks_process) == num_blocks_process
     for block in blocks_process:
diff --git a/tests/tests_utils/test_2_oton/test_3_converter_1_local.py b/tests/tests_utils/test_2_oton/test_3_converter_1_local.py
index e113bcaa..1232a756 100644
--- a/tests/tests_utils/test_2_oton/test_3_converter_1_local.py
+++ b/tests/tests_utils/test_2_oton/test_3_converter_1_local.py
@@ -9,20 +9,20 @@
 
 def test_convert_wf1_with_env_local(oton_converter):
     nextflow_file_class = oton_converter.convert_oton(IN_TXT_WF1, OUT_NF_WF1_LOCAL, "local", False)
-    assert 'params.input_file_group = "OCR-D-IMG"' in nextflow_file_class.nf_lines_parameters
+    assert nextflow_file_class.nf_lines_parameters['params.input_file_group'] == '"OCR-D-IMG"'
     assert_common_features(nextflow_file_class, 8, 1, False)
     assert_compare_workflow_blocks(OUT_NF_WF1_LOCAL, EXPECTED_WF1)
 
 def test_convert_wf1_with_env_local_with_mets_server(oton_converter):
     nextflow_file_class = oton_converter.convert_oton(IN_TXT_WF1, OUT_NF_WF1_LOCAL_WITH_MS, "local", True)
-    assert 'params.input_file_group = "OCR-D-IMG"' in nextflow_file_class.nf_lines_parameters
+    assert nextflow_file_class.nf_lines_parameters['params.input_file_group'] == '"OCR-D-IMG"'
     assert_common_features(nextflow_file_class, 8, 1, True)
     assert_compare_workflow_blocks(OUT_NF_WF1_LOCAL_WITH_MS, EXPECTED_WF1_WITH_MS)
 
 
 def test_convert_wf2_with_env_local(oton_converter):
     nextflow_file_class = oton_converter.convert_oton(IN_TXT_WF2, OUT_NF_WF2_LOCAL, "local", False)
-    assert 'params.input_file_group = "OCR-D-IMG"' in nextflow_file_class.nf_lines_parameters
+    assert nextflow_file_class.nf_lines_parameters['params.input_file_group'] == '"OCR-D-IMG"'
     assert_common_features(nextflow_file_class, 7, 1, False)
     assert_common_features_local(nextflow_file_class)
     assert_compare_workflow_blocks(OUT_NF_WF2_LOCAL, EXPECTED_WF2)
@@ -30,7 +30,7 @@ def test_convert_wf2_with_env_local(oton_converter):
 
 def test_convert_wf3_with_env_local(oton_converter):
     nextflow_file_class = oton_converter.convert_oton(IN_TXT_WF3, OUT_NF_WF3_LOCAL, "local", False)
-    assert 'params.input_file_group = "OCR-D-GT-SEG-BLOCK,OCR-D-OCR"' in nextflow_file_class.nf_lines_parameters
+    assert nextflow_file_class.nf_lines_parameters['params.input_file_group'] == '"OCR-D-GT-SEG-BLOCK,OCR-D-OCR"'
     assert_common_features(nextflow_file_class, 3, 1, False)
     assert_common_features_local(nextflow_file_class)
     assert_compare_workflow_blocks(OUT_NF_WF3_LOCAL, EXPECTED_WF3)
@@ -38,7 +38,7 @@ def test_convert_wf3_with_env_local(oton_converter):
 
 def test_convert_wf4_with_env_local(oton_converter):
     nextflow_file_class = oton_converter.convert_oton(IN_TXT_WF4, OUT_NF_WF4_LOCAL, "local", False)
-    assert 'params.input_file_group = "OCR-D-IMG"' in nextflow_file_class.nf_lines_parameters
+    assert nextflow_file_class.nf_lines_parameters['params.input_file_group'] == '"OCR-D-IMG"'
     assert_common_features(nextflow_file_class, 13, 1, False)
     assert_common_features_local(nextflow_file_class)
     assert_compare_workflow_blocks(OUT_NF_WF4_LOCAL, EXPECTED_WF4)

From 602636edc5f484e3430f15d5ad6a7711992424bc Mon Sep 17 00:00:00 2001
From: Mehmed Mustafa <mehmed.n.mustafa@gmail.com>
Date: Mon, 2 Dec 2024 16:20:20 +0100
Subject: [PATCH 16/16] fix: operandi_utils setup

---
 src/utils/setup.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/utils/setup.py b/src/utils/setup.py
index 9a79e4db..77b08639 100644
--- a/src/utils/setup.py
+++ b/src/utils/setup.py
@@ -20,7 +20,9 @@
         'operandi_utils.oton',
         'operandi_utils.rabbitmq'
     ],
-    package_data={'': ['batch_scripts/*.sh', 'nextflow_workflows/*.nf', 'ocrd_all_tool.json']},
+    package_data={
+        '': ['batch_scripts/*.sh', 'nextflow_workflows/*.nf', 'ocrd_process_workflows/*.txt', 'ocrd_all_tool.json']
+    },
     install_requires=install_requires,
     entry_points={
         'console_scripts': [