From eec909fdfb763ffc102540174512b8f2390b927a Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 12:57:43 +0000
Subject: [PATCH 01/14] add first version module

---
 .../foldmason/createdb/environment.yml        |  7 ++
 modules/nf-core/foldmason/createdb/main.nf    | 45 +++++++++++
 modules/nf-core/foldmason/createdb/meta.yml   | 48 ++++++++++++
 .../foldmason/createdb/tests/main.nf.test     | 74 +++++++++++++++++++
 4 files changed, 174 insertions(+)
 create mode 100644 modules/nf-core/foldmason/createdb/environment.yml
 create mode 100644 modules/nf-core/foldmason/createdb/main.nf
 create mode 100644 modules/nf-core/foldmason/createdb/meta.yml
 create mode 100644 modules/nf-core/foldmason/createdb/tests/main.nf.test

diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
new file mode 100644
index 00000000000..f0aa69920ee
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::foldmason=2.7bd21ed"
diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
new file mode 100644
index 00000000000..4768a5abf8e
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -0,0 +1,45 @@
+process FOLDMASON_CREATEDB {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/foldmason:512dd7b3e2453a75"
+
+    input:
+    tuple val(meta) , path(pdbs)
+
+    output:
+    tuple val(meta), path("${prefix}*"), emit: db
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    foldmason createdb \\
+        ${pdbs} \\
+        ${prefix} \\
+        $args \\
+        --threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/modules/nf-core/foldmason/createdb/meta.yml
new file mode 100644
index 00000000000..7fd4f5e25f0
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/meta.yml
@@ -0,0 +1,48 @@
+name: "foldmason_easymsa"
+description: Creates a database for Foldmason.
+keywords:
+  - alignment
+  - MSA
+  - genomics
+  - structure
+tools:
+  - "foldmason":
+      description: "Multiple Protein Structure Alignment at Scale with FoldMason"
+      homepage: "https://github.com/steineggerlab/foldmason"
+      documentation: "https://github.com/steineggerlab/foldmason"
+      tool_dev_url: "https://github.com/steineggerlab/foldmason"
+      doi: "10.1101/2024.08.01.606130"
+      licence: ["GPL v3"]
+      identifier: biotools:foldmason
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - pdbs:
+        type: file
+        description: Input protein structures in PDB format.
+        pattern: "*.{pdb,mmcif}"
+
+output:
+  - db:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${prefix}":
+          type: files
+          description: All database files created by Foldmason
+          pattern: "*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@luisas"
+maintainers:
+  - "@luisas"
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test b/modules/nf-core/foldmason/createdb/tests/main.nf.test
new file mode 100644
index 00000000000..d3e418b239b
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test
@@ -0,0 +1,74 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test foldmason/createdb
+nextflow_process {
+
+    name "Test Process FOLDMASON_CREATEDB"
+    script "../main.nf"
+    process "FOLDMASON_CREATEDB"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "foldmason"
+    tag "foldmason/createdb"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}

From b37087e5215c41ee2b99a0994579f389027ffda3 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 12:59:56 +0000
Subject: [PATCH 02/14] add test

---
 .../foldmason/createdb/tests/main.nf.test     | 52 ++++++++-----------
 1 file changed, 23 insertions(+), 29 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test b/modules/nf-core/foldmason/createdb/tests/main.nf.test
index d3e418b239b..6af8798fbad 100644
--- a/modules/nf-core/foldmason/createdb/tests/main.nf.test
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test
@@ -10,63 +10,57 @@ nextflow_process {
     tag "modules_nfcore"
     tag "foldmason"
     tag "foldmason/createdb"
+    tag  "untar"
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("sarscov2 - bam") {
+    setup {
 
-        // TODO nf-core: If you are created a test for a chained module
-        // (the module requires running more than one process to generate the required output)
-        // add the 'setup' method here.
-        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+        run("UNTAR") {
+            script "../../../../../modules/nf-core/untar/main.nf"
+                process {
+                    """
+                        archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                        input[0] = Channel.of(tuple([id:'test'], archive))
+                    """
+                }
+        }
+    }
+
+    test("seatoxin") {
 
         when {
+
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                ]
+                    input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
                 """
             }
         }
 
         then {
             assertAll(
-                { assert process.success },
+                { assert process.success  },
                 { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
-            )
+                )
         }
 
     }
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
-    test("sarscov2 - bam - stub") {
-
-        options "-stub"
+    test("seatoxin - stub ") {
 
         when {
+
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                ]
+                    input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
                 """
             }
         }
 
         then {
             assertAll(
-                { assert process.success },
+                { assert process.success  },
                 { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-            )
+                )
         }
 
     }

From 1f8f61a1bd6fda108cfd0e641ba5579720c20c40 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 13:05:06 +0000
Subject: [PATCH 03/14] add tests

---
 .../createdb/tests/main.nf.test.snap          | 128 ++++++++++++++++++
 1 file changed, 128 insertions(+)
 create mode 100644 modules/nf-core/foldmason/createdb/tests/main.nf.test.snap

diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
new file mode 100644
index 00000000000..72a19f06faa
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
@@ -0,0 +1,128 @@
+{
+    "seatoxin - stub ": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T13:01:24.368817354"
+    },
+    "seatoxin": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T13:01:14.71331904"
+    }
+}
\ No newline at end of file

From 960ce8735a8b9167e035aec6ee521df4b5bf7316 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 13:11:35 +0000
Subject: [PATCH 04/14] add

---
 modules/nf-core/foldmason/createdb/meta.yml           | 6 +++---
 modules/nf-core/foldmason/createdb/tests/main.nf.test | 2 --
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/modules/nf-core/foldmason/createdb/meta.yml
index 7fd4f5e25f0..06a47d43296 100644
--- a/modules/nf-core/foldmason/createdb/meta.yml
+++ b/modules/nf-core/foldmason/createdb/meta.yml
@@ -1,4 +1,4 @@
-name: "foldmason_easymsa"
+name: "foldmason_createdb"
 description: Creates a database for Foldmason.
 keywords:
   - alignment
@@ -33,8 +33,8 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "${prefix}":
-          type: files
+      - "${prefix}*":
+          type: file
           description: All database files created by Foldmason
           pattern: "*"
   - versions:
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test b/modules/nf-core/foldmason/createdb/tests/main.nf.test
index 6af8798fbad..9ac567a7504 100644
--- a/modules/nf-core/foldmason/createdb/tests/main.nf.test
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test foldmason/createdb
 nextflow_process {
 
     name "Test Process FOLDMASON_CREATEDB"

From ec468d98c5e398abfd7816d85f8ebd225b0d156d Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 13:12:17 +0000
Subject: [PATCH 05/14] ass

---
 modules/nf-core/foldmason/createdb/environment.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
index f0aa69920ee..92326c3d851 100644
--- a/modules/nf-core/foldmason/createdb/environment.yml
+++ b/modules/nf-core/foldmason/createdb/environment.yml
@@ -1,5 +1,3 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

From 232fa50fe11cb20dfd33af0f55196fab0c57536a Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 13:28:26 +0000
Subject: [PATCH 06/14] add

---
 modules/nf-core/foldmason/createdb/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
index 92326c3d851..80d4dd371d9 100644
--- a/modules/nf-core/foldmason/createdb/environment.yml
+++ b/modules/nf-core/foldmason/createdb/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::foldmason=2.7bd21ed"
+  - bioconda::foldmason=2.7bd21ed

From 47724817a149508f87f0acc241274e4cf0da0e40 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 13:56:35 +0000
Subject: [PATCH 07/14] up

---
 modules/nf-core/foldmason/createdb/environment.yml | 2 +-
 modules/nf-core/foldmason/createdb/main.nf         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
index 80d4dd371d9..213cb2984c4 100644
--- a/modules/nf-core/foldmason/createdb/environment.yml
+++ b/modules/nf-core/foldmason/createdb/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::foldmason=2.7bd21ed
+  - bioconda::foldmason=1.763a428
diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
index 4768a5abf8e..ac9334ba846 100644
--- a/modules/nf-core/foldmason/createdb/main.nf
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -10,7 +10,7 @@ process FOLDMASON_CREATEDB {
 
     output:
     tuple val(meta), path("${prefix}*"), emit: db
-    path "versions.yml"               , emit: versions
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From d8e2614fb74c10f0d71608f00748501625cf5b96 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 15:01:45 +0000
Subject: [PATCH 08/14] update containers

---
 modules/nf-core/foldmason/createdb/environment.yml | 2 +-
 modules/nf-core/foldmason/createdb/main.nf         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
index 213cb2984c4..80d4dd371d9 100644
--- a/modules/nf-core/foldmason/createdb/environment.yml
+++ b/modules/nf-core/foldmason/createdb/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::foldmason=1.763a428
+  - bioconda::foldmason=2.7bd21ed
diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
index ac9334ba846..a78c50d8f91 100644
--- a/modules/nf-core/foldmason/createdb/main.nf
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -3,7 +3,7 @@ process FOLDMASON_CREATEDB {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/foldmason:512dd7b3e2453a75"
+    container "community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d"
 
     input:
     tuple val(meta) , path(pdbs)

From 7276cf4dbf712083b69ad79dbfa0e7d0754d6de3 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 15:13:39 +0000
Subject: [PATCH 09/14] update version

---
 modules/nf-core/foldmason/createdb/main.nf           |  4 +++-
 .../foldmason/createdb/tests/main.nf.test.snap       | 12 ++++++------
 modules/nf-core/foldmason/easymsa/environment.yml    |  4 +---
 modules/nf-core/foldmason/easymsa/main.nf            |  5 ++++-
 4 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
index a78c50d8f91..8376a658a1a 100644
--- a/modules/nf-core/foldmason/createdb/main.nf
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -3,7 +3,9 @@ process FOLDMASON_CREATEDB {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'oras://community.wave.seqera.io/library/foldmason:2.7bd21ed--a45f76ed12b391e6':
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
 
     input:
     tuple val(meta) , path(pdbs)
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
index 72a19f06faa..dce5175dc90 100644
--- a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
@@ -26,7 +26,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
                 ],
                 "db": [
                     [
@@ -52,7 +52,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
                 ]
             }
         ],
@@ -60,7 +60,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-09T13:01:24.368817354"
+        "timestamp": "2024-12-09T15:11:27.426024133"
     },
     "seatoxin": {
         "content": [
@@ -89,7 +89,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
                 ],
                 "db": [
                     [
@@ -115,7 +115,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e7bf0507f95974b4e2b838dc7fcee500"
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
                 ]
             }
         ],
@@ -123,6 +123,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-09T13:01:14.71331904"
+        "timestamp": "2024-12-09T15:11:15.375341633"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml
index 64a5b3671d4..fa2909a9491 100644
--- a/modules/nf-core/foldmason/easymsa/environment.yml
+++ b/modules/nf-core/foldmason/easymsa/environment.yml
@@ -1,8 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::foldmason=1.763a428
+  - bioconda::foldmason=2.7bd21ed
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf
index bb1737f05ef..1ae97413e93 100644
--- a/modules/nf-core/foldmason/easymsa/main.nf
+++ b/modules/nf-core/foldmason/easymsa/main.nf
@@ -3,7 +3,10 @@ process FOLDMASON_EASYMSA {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/foldmason_pigz:54849036d93c89ed"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03':
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+
 
     input:
     tuple val(meta) , path(pdbs)

From 3ed54721c262efd6f377572b09ceae830e9e26ac Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 15:24:31 +0000
Subject: [PATCH 10/14] update version easymsa

---
 modules/nf-core/foldmason/easymsa/main.nf     |  2 +-
 .../foldmason/easymsa/tests/main.nf.test.snap | 32 +++++++++----------
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf
index 1ae97413e93..b4870da0d10 100644
--- a/modules/nf-core/foldmason/easymsa/main.nf
+++ b/modules/nf-core/foldmason/easymsa/main.nf
@@ -5,7 +5,7 @@ process FOLDMASON_EASYMSA {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
             'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03':
-            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+            'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }"
 
 
     input:
diff --git a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap
index 384d2021284..4951f29bff3 100644
--- a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap
+++ b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
@@ -38,7 +38,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -46,7 +46,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:56:12.836231763"
+        "timestamp": "2024-12-09T15:22:29.135105042"
     },
     "Test on seatoxin dataset - uncompressed": {
         "content": [
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
@@ -87,7 +87,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -95,7 +95,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:55:41.89060384"
+        "timestamp": "2024-12-09T15:21:46.797852094"
     },
     "Test on seatoxin dataset - compressed": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
@@ -136,7 +136,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -144,7 +144,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:55:52.135344443"
+        "timestamp": "2024-12-09T15:21:58.958099076"
     },
     "Test on seatoxin dataset - guide_tree": {
         "content": [
@@ -154,7 +154,7 @@
                         {
                             "id": "test"
                         },
-                        "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4"
+                        "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08"
                     ]
                 ],
                 "1": [
@@ -162,18 +162,18 @@
                         {
                             "id": "test"
                         },
-                        "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae"
+                        "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4"
+                        "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08"
                     ]
                 ],
                 "msa_aa": [
@@ -181,11 +181,11 @@
                         {
                             "id": "test"
                         },
-                        "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae"
+                        "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -193,6 +193,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:56:02.473496089"
+        "timestamp": "2024-12-09T15:22:11.0778334"
     }
 }
\ No newline at end of file

From da06679f578ecaf274f63ea3c9bfb65959d9d58b Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 16:34:20 +0100
Subject: [PATCH 11/14] Update modules/nf-core/foldmason/createdb/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 modules/nf-core/foldmason/createdb/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
index 8376a658a1a..09d0c50d335 100644
--- a/modules/nf-core/foldmason/createdb/main.nf
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -8,7 +8,7 @@ process FOLDMASON_CREATEDB {
             'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
 
     input:
-    tuple val(meta) , path(pdbs)
+    tuple val(meta) , path(structures)
 
     output:
     tuple val(meta), path("${prefix}*"), emit: db

From 7a564cc7a4aa90ac9a0e2140738b664e0c976749 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 16:34:28 +0100
Subject: [PATCH 12/14] Update modules/nf-core/foldmason/createdb/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 modules/nf-core/foldmason/createdb/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/modules/nf-core/foldmason/createdb/meta.yml
index 06a47d43296..fd47efe2f90 100644
--- a/modules/nf-core/foldmason/createdb/meta.yml
+++ b/modules/nf-core/foldmason/createdb/meta.yml
@@ -21,9 +21,9 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. `[ id:'sample1', single_end:false ]`
-    - pdbs:
+    - structures:
         type: file
-        description: Input protein structures in PDB format.
+        description: Input protein structures in `PDB` or `mmCIF` format.
         pattern: "*.{pdb,mmcif}"
 
 output:

From 19baac3ed8b01a2b5c352ef74cbd6c85526fb6d5 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 16:34:33 +0100
Subject: [PATCH 13/14] Update modules/nf-core/foldmason/createdb/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 modules/nf-core/foldmason/createdb/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
index 09d0c50d335..dda43b07c65 100644
--- a/modules/nf-core/foldmason/createdb/main.nf
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -22,7 +22,7 @@ process FOLDMASON_CREATEDB {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     foldmason createdb \\
-        ${pdbs} \\
+        ${structures} \\
         ${prefix} \\
         $args \\
         --threads $task.cpus

From d67359cfc1e2c19f83341b870542ca6b6ef30438 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Mon, 9 Dec 2024 17:15:57 +0100
Subject: [PATCH 14/14] Update modules/nf-core/foldmason/createdb/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 modules/nf-core/foldmason/createdb/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
index dda43b07c65..c54b45f3f06 100644
--- a/modules/nf-core/foldmason/createdb/main.nf
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -4,7 +4,7 @@ process FOLDMASON_CREATEDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'oras://community.wave.seqera.io/library/foldmason:2.7bd21ed--a45f76ed12b391e6':
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' :
             'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
 
     input: