From 691393e0c98759dc85a0f5513fd11e2be7f10cb7 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 12 Dec 2024 10:50:10 +0100
Subject: [PATCH 1/7] bump versions and fix missing args and command formatting

---
 .../nf-core/centrifuge/build/environment.yml  |  3 +-
 modules/nf-core/centrifuge/build/main.nf      | 28 +++++++------
 .../centrifuge/build/tests/main.nf.test.snap  |  6 +--
 .../centrifuge/centrifuge/environment.yml     |  3 +-
 modules/nf-core/centrifuge/centrifuge/main.nf | 42 ++++++++++---------
 .../centrifuge/kreport/environment.yml        |  3 +-
 modules/nf-core/centrifuge/kreport/main.nf    | 17 ++++----
 7 files changed, 56 insertions(+), 46 deletions(-)

diff --git a/modules/nf-core/centrifuge/build/environment.yml b/modules/nf-core/centrifuge/build/environment.yml
index 42592891580..b49177e9759 100644
--- a/modules/nf-core/centrifuge/build/environment.yml
+++ b/modules/nf-core/centrifuge/build/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/build/main.nf b/modules/nf-core/centrifuge/build/main.nf
index b767040de7f..02cfd8ccf92 100644
--- a/modules/nf-core/centrifuge/build/main.nf
+++ b/modules/nf-core/centrifuge/build/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_BUILD {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(fasta)
@@ -15,8 +15,8 @@ process CENTRIFUGE_BUILD {
     path size_table
 
     output:
-    tuple val(meta), path("${prefix}/") , emit: cf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${prefix}/"), emit: cf
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,13 +29,15 @@ process CENTRIFUGE_BUILD {
     mkdir ${prefix}
 
     centrifuge-build \\
-        -p $task.cpus \\
-        $fasta \\
+        -p ${task.cpus} \\
+        ${fasta} \\
         ${prefix}/${prefix} \\
-        --conversion-table $conversion_table \\
-        --taxonomy-tree $taxonomy_tree \\
-        --name-table $name_table \\
-        ${size_table_cmd}
+        --conversion-table ${conversion_table} \\
+        --taxonomy-tree ${taxonomy_tree} \\
+        --name-table ${name_table} \\
+        ${size_table_cmd} \\
+        ${args} \\
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,7 +46,7 @@ process CENTRIFUGE_BUILD {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p ${prefix}/
diff --git a/modules/nf-core/centrifuge/build/tests/main.nf.test.snap b/modules/nf-core/centrifuge/build/tests/main.nf.test.snap
index fa7d1dc3682..4a7b1247d38 100644
--- a/modules/nf-core/centrifuge/build/tests/main.nf.test.snap
+++ b/modules/nf-core/centrifuge/build/tests/main.nf.test.snap
@@ -80,9 +80,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-02-15T10:10:19.439629103"
+        "timestamp": "2024-12-12T10:38:44.613715625"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml
index 42592891580..b49177e9759 100644
--- a/modules/nf-core/centrifuge/centrifuge/environment.yml
+++ b/modules/nf-core/centrifuge/centrifuge/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
index d9a5653df56..f287dc25c23 100644
--- a/modules/nf-core/centrifuge/centrifuge/main.nf
+++ b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_CENTRIFUGE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(reads)
@@ -14,12 +14,12 @@ process CENTRIFUGE_CENTRIFUGE {
     val save_aligned
 
     output:
-    tuple val(meta), path('*report.txt')                 , emit: report
-    tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
-    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
-    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path('*report.txt'), emit: report
+    tuple val(meta), path('*results.txt'), emit: results
+    tuple val(meta), path('*.{sam,tab}'), optional: true, emit: sam
+    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_mapped
+    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_unmapped
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,13 +27,14 @@ process CENTRIFUGE_CENTRIFUGE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
@@ -49,13 +50,13 @@ process CENTRIFUGE_CENTRIFUGE {
     centrifuge \\
         -x \$db_name \\
         --temp-directory ./temp \\
-        -p $task.cpus \\
-        $paired \\
+        -p ${task.cpus} \\
+        ${paired} \\
         --report-file ${prefix}.report.txt \\
         -S ${prefix}.results.txt \\
-        $unaligned \\
-        $aligned \\
-        $args
+        ${unaligned} \\
+        ${aligned} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -64,15 +65,16 @@ process CENTRIFUGE_CENTRIFUGE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def _paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml
index 42592891580..b49177e9759 100644
--- a/modules/nf-core/centrifuge/kreport/environment.yml
+++ b/modules/nf-core/centrifuge/kreport/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf
index 25eb7167b7c..b7e83604950 100644
--- a/modules/nf-core/centrifuge/kreport/main.nf
+++ b/modules/nf-core/centrifuge/kreport/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_KREPORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(report)
@@ -13,7 +13,7 @@ process CENTRIFUGE_KREPORT {
 
     output:
     tuple val(meta), path('*.txt'), emit: kreport
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,7 +23,10 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
-    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
+    centrifuge-kreport \\
+        ${args} \\
+        -x \$db_name \\
+        ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -32,7 +35,7 @@ process CENTRIFUGE_KREPORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

From 3644e04afd7ccced03200f04dfc291d8cb8bc05e Mon Sep 17 00:00:00 2001
From: Sateesh <perisateesh@gmail.com>
Date: Fri, 13 Dec 2024 07:23:44 +0000
Subject: [PATCH 2/7] CI: docker self hosted - userEmulate and dont
 fixOwnership

---
 tests/config/nf-test.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 32966754152..61a9a981d52 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -29,8 +29,8 @@ profiles {
     }
     docker_self_hosted {
         docker.enabled          = true
-        docker.userEmulation    = false
-        docker.fixOwnership     = true
+        docker.userEmulation    = true
+        docker.fixOwnership     = false
         docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges'
     }
     arm {

From 560b8884bd9c5365d50cb280abfccf9a66ad438d Mon Sep 17 00:00:00 2001
From: Sateesh <perisateesh@gmail.com>
Date: Fri, 13 Dec 2024 07:34:31 +0000
Subject: [PATCH 3/7] try suggestion from claude

---
 tests/config/nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 61a9a981d52..d8a53861be9 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -31,7 +31,7 @@ profiles {
         docker.enabled          = true
         docker.userEmulation    = true
         docker.fixOwnership     = false
-        docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges'
+        docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges --cgroup-parent=/docker --userns=host'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 493e82100e83b48214b2804537ffcec8223d499a Mon Sep 17 00:00:00 2001
From: Sateesh <perisateesh@gmail.com>
Date: Fri, 13 Dec 2024 07:38:44 +0000
Subject: [PATCH 4/7] fix cgroup parent slice

---
 tests/config/nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index d8a53861be9..5f8a1a30c6b 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -31,7 +31,7 @@ profiles {
         docker.enabled          = true
         docker.userEmulation    = true
         docker.fixOwnership     = false
-        docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges --cgroup-parent=/docker --userns=host'
+        docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges --cgroup-parent=/system.slice --userns=host'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 23bb3f623a0bc0e6dad25eede4231b7728fa56bb Mon Sep 17 00:00:00 2001
From: Sateesh <perisateesh@gmail.com>
Date: Fri, 13 Dec 2024 07:42:02 +0000
Subject: [PATCH 5/7] rm cgroup parent slice

---
 tests/config/nf-test.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 5f8a1a30c6b..249dc4db3e7 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -29,9 +29,9 @@ profiles {
     }
     docker_self_hosted {
         docker.enabled          = true
-        docker.userEmulation    = true
-        docker.fixOwnership     = false
-        docker.runOptions       = '--platform=linux/amd64 --security-opt=no-new-privileges --cgroup-parent=/system.slice --userns=host'
+        docker.userEmulation    = false
+        docker.fixOwnership     = true
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64 --security-opt=no-new-privileges'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 904976944bcac7831421e9b912365c45425d2171 Mon Sep 17 00:00:00 2001
From: Sateesh <perisateesh@gmail.com>
Date: Fri, 13 Dec 2024 08:09:18 +0000
Subject: [PATCH 6/7] rm security opts

---
 tests/config/nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 249dc4db3e7..a3614034fee 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -31,7 +31,7 @@ profiles {
         docker.enabled          = true
         docker.userEmulation    = false
         docker.fixOwnership     = true
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64 --security-opt=no-new-privileges'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 58336433a45b033c5adcdd79758b48607e69a3e6 Mon Sep 17 00:00:00 2001
From: Sateesh <perisateesh@gmail.com>
Date: Fri, 13 Dec 2024 08:17:31 +0000
Subject: [PATCH 7/7] userns n security opts

---
 tests/config/nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index a3614034fee..7f5f0082766 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -31,7 +31,7 @@ profiles {
         docker.enabled          = true
         docker.userEmulation    = false
         docker.fixOwnership     = true
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64  --security-opt=no-new-privileges --userns=host'
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'