Merge branch 'master' into toulligqc

nf-core · Dec 10, 2024 · 22207e0 · 22207e0
2 parents d5f879b + 2edb630
commit 22207e0
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Showing 23 changed files with 681 additions and 61 deletions.
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -108,13 +108,18 @@ jobs:
     needs: [nf-test-gpu]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -32,7 +32,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -110,13 +110,18 @@ jobs:
     needs: [nf-test]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |

diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test
@@ -117,5 +117,4 @@ nextflow_process {
             )
         }
     }
-
 }
diff --git a/modules/nf-core/deseq2/differential/main.nf b/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:
     """

diff --git a/.../deseq2/differential/templates/deseq_de.R → ...ferential/templates/deseq2_differential.R b/.../deseq2/differential/templates/deseq_de.R → ...ferential/templates/deseq2_differential.R
diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
@@ -0,0 +1,5 @@
+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
@@ -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
+    """
+}
diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/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"
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test b/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() }
+                )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap 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:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ],
+                "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"
+    }
+}
diff --git 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
@@ -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)
-Original file line number
+Diff line change
@@ Expand Up / @@ -117,5 +117,4 @@ nextflow_process { @@
                 )
             }
         }
     }