Merge branch 'master' into das_tool

.github/conda_skip.yml

@@ -182,3 +182,5 @@ exclude:
     path: modules/nf-core/xeniumranger/resegment
   - profile: conda
     path: modules/nf-core/xeniumranger/import-segmentation
+  - profile: conda
+    path: modules/nf-core/parabricks/genotypegvcf

.github/workflows/lint.yml

@@ -109,7 +109,7 @@ jobs:
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+      - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
         id: cache-pip
         with:
           path: ~/.cache/pip

.github/workflows/pytest-workflow.yml

@@ -247,7 +247,7 @@ jobs:
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+      - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
         id: cache-pip-pytest
         with:
           path: ~/.cache/pip

.github/workflows/wave.yml

@@ -31,7 +31,7 @@ jobs:
 
       - name: Find conda differences
         id: conda-diff
-        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
+        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
         with:
           json: true
           escape_json: false
@@ -40,7 +40,7 @@ jobs:
 
       - name: Find Dockerfile differences
         id: docker-diff
-        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
+        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
         with:
           json: true
           escape_json: false

modules/nf-core/deseq2/differential/main.nf

@@ -29,7 +29,7 @@ process DESEQ2_DIFFERENTIAL {
     task.ext.when == null || task.ext.when
 
     script:
-    template 'deseq_de.R'
+    template 'deseq2_differential.R'
 
     stub:
     """

modules/nf-core/foldmason/createdb/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::foldmason=2.7bd21ed

modules/nf-core/foldmason/createdb/main.nf

@@ -0,0 +1,47 @@
+process FOLDMASON_CREATEDB {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' :
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+
+    input:
+    tuple val(meta) , path(structures)
+
+    output:
+    tuple val(meta), path("${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 \\
+        ${structures} \\
+        ${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
+    """
+}

modules/nf-core/foldmason/createdb/meta.yml

@@ -0,0 +1,48 @@
+name: "foldmason_createdb"
+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 ]`
+    - structures:
+        type: file
+        description: Input protein structures in `PDB` or `mmCIF` format.
+        pattern: "*.{pdb,mmcif}"
+
+output:
+  - db:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${prefix}*":
+          type: file
+          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"

modules/nf-core/foldmason/createdb/tests/main.nf.test

@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process FOLDMASON_CREATEDB"
+    script "../main.nf"
+    process "FOLDMASON_CREATEDB"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "foldmason"
+    tag "foldmason/createdb"
+    tag  "untar"
+
+    setup {
+
+        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 {
+                """
+                    input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success  },
+                { assert snapshot(process.out).match() }
+                )
+        }
+
+    }
+
+    test("seatoxin - stub ") {
+
+        when {
+
+            process {
+                """
+                    input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success  },
+                { assert snapshot(process.out).match() }
+                )
+        }
+
+    }
+
+}

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:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ],
+                "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:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T15:11:27.426024133"
+    },
+    "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:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ],
+                "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:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T15:11:15.375341633"
+    }
+}

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

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_pigz:88809eb5649534b0' }"
+
 
     input:
     tuple val(meta) , path(pdbs)