Merge branch 'master' into deprecate_custom_getchromsizes

.github/actions/nf-test-action/action.yml

@@ -73,8 +73,8 @@ runs:
         SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
         SENTIEON_AUTH_MECH: "GitHub Actions - token"
         TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
-        NFT_WORKDIR: "~"
       run: |
+        NFT_WORKDIR=~ \
         nf-test test \
           --profile=${{ inputs.profile }} \
           --tap=test.tap \

.github/scripts/wave_singularity.py

@@ -4,6 +4,7 @@
 # dependencies = [
 #     "requests",
 #     "rich",
+#     "rich_click"
 # ]
 # ///
 

.github/workflows/gpu-tests.yml

@@ -43,13 +43,17 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       # Expose detected tags as 'modules' and 'workflows' output variables
-      paths: ${{ steps.list.outputs.components }}
+      paths: ${{ steps.outputs.outputs.components }}
       modules: ${{ steps.outputs.outputs.modules }}
       subworkflows: ${{ steps.outputs.outputs.subworkflows}}
       # Prod for version bumping
     steps:
       - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        uses: AutoModality/[email protected]
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0
@@ -70,7 +74,7 @@ jobs:
           echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT
       - name: debug
         run: |
-          echo ${{ steps.filter.outputs.components }}
+          echo ${{ steps.outputs.outputs.components }}
           echo ${{ steps.outputs.outputs.modules }}
           echo ${{ steps.outputs.outputs.subworkflows }}
 

.github/workflows/lint.yml

@@ -50,9 +50,11 @@ jobs:
     name: nf-core-changes
     runs-on: ubuntu-latest
     outputs:
-      tags: ${{ steps.filter.outputs.changes }}
-      modules: ${{ steps.tags.outputs.modules }}
-      subworkflows: ${{ steps.tags.outputs.subworkflows }}
+      # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files
+      modules: ${{ steps.filter.outputs.modules }}
+      modules_files: ${{ steps.module_names.outputs.result }}
+      subworkflows: ${{ steps.filter.outputs.subworkflows }}
+      subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
         with:
@@ -61,29 +63,46 @@ jobs:
       - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
         id: filter
         with:
-          filters: "tests/config/pytest_modules.yml"
+          filters: |
+            modules:
+              - 'modules/nf-core/**'
+              - 'tests/modules/nf-core/**'
+            subworkflows:
+              - 'subworkflows/nf-core/**'
+              - 'tests/subworkflows/nf-core/**'
           token: ""
+          list-files: "json"
 
-      - name: Fetch module tags
-        id: tags
-        run: |
-          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
-          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
+      - name: Get module name
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        id: module_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.modules_files }}.map(path => path.replace('modules/nf-core/', '').split('/').slice(0,2).filter(x => x !== 'main.nf').join('/')))];
+
+      - name: Get subworkflow name
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        id: subworkflow_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}.map(path => path.replace('subworkflows/nf-core/', '').split('/').slice(0,2).filter(x => x !== 'main.nf').join('/')))];
 
       - name: debug
         run: |
-          echo ${{ steps.tags.outputs.modules }}
-          echo ${{ steps.tags.outputs.subworkflows }}
+          echo ${{ steps.filter.outputs.modules_files }}
+          echo ${{ steps.filter.outputs.subworkflows_files }}
+          echo ${{ steps.module_names.outputs.result }}
+          echo ${{ steps.subworkflow_names.outputs.result }}
 
   nf-core-lint-modules:
     runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
     name: nf-core lint modules
     needs: nf-core-changes
-    if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }}
+    if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }}
     strategy:
       fail-fast: false
       matrix:
-        tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}"
+        module: "${{ fromJson(needs.nf-core-changes.outputs.modules_files) }}"
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
@@ -114,18 +133,18 @@ jobs:
       - name: Install nf-core tools development version
         run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
 
-      - name: Lint module ${{ matrix.tags }}
-        run: nf-core modules lint ${{ matrix.tags }}
+      - name: Lint module ${{ matrix.module }}
+        run: nf-core modules lint ${{ matrix.module }}
 
   nf-core-lint-subworkflows:
     runs-on: ubuntu-latest
     name: nf-core lint subworkflows
     needs: nf-core-changes
-    if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }}
+    if: ${{ (needs.nf-core-changes.outputs.subworkflows == 'true') }}
     strategy:
       fail-fast: false
       matrix:
-        tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}"
+        subworkflow: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files) }}"
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
@@ -148,8 +167,8 @@ jobs:
       - name: Install nf-core tools development version
         run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
 
-      - name: Lint module ${{ matrix.tags }}
-        run: nf-core subworkflows lint ${{ matrix.tags }}
+      - name: Lint subworkflow ${{ matrix.subworkflow }}
+        run: nf-core subworkflows lint ${{ matrix.subworkflow }}
 
   confirm-pass:
     runs-on: ubuntu-latest

.github/workflows/nf-test.yml

@@ -63,7 +63,11 @@ jobs:
       SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
     steps:
       - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        uses: AutoModality/[email protected]
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0

.github/workflows/wave.yml

@@ -88,15 +88,14 @@ jobs:
     # if: github.repository == 'nf-core/modules'
     if: ${{ needs.generate-matrix.outputs.docker-matrix != '[]' }}
     needs: generate-matrix
-    name: Build Dockerfile-based ${{ matrix.profile }} Container
+    name: Build Dockerfile-based Container
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       fail-fast: false
       max-parallel: 4
       matrix:
         files: "${{ fromJson(needs.generate-matrix.outputs.docker-matrix) }}"
-        profile: [docker, singularity]
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
@@ -117,11 +116,8 @@ jobs:
       - name: Build ${{ matrix.profile }} container
         # NOTE If you're changing a Dockerfile and this is running, try to update the Dockerfile to build with wave
         continue-on-error: false
-        env:
-          PROFILE: ${{ (contains(matrix.profile, 'singularity') && '--singularity') || '' }}
         run: |
           wave -f "${{ matrix.files }}" \
-              $PROFILE \
               --freeze \
               --await \
               --build-repo quay.io/nf-core/modules/${{steps.registry-name.outputs.result}} \

modules/nf-core/regtools/junctionsextract/environment.yml

@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::regtools=0.5.0"

modules/nf-core/regtools/junctionsextract/main.nf

@@ -0,0 +1,45 @@
+process REGTOOLS_JUNCTIONSEXTRACT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::regtools=0.5.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b6c0653189b95b22e16038f61ade205a865857f54eeae9ba0184490a1834f7c9/data' :
+        'community.wave.seqera.io/library/regtools:0.5.0--b9a260c4c898354a' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path("*.junc"), emit: junc
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    regtools junctions extract \\
+        $args \\
+        -o ${prefix}.junc \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.junc
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
+    END_VERSIONS
+    """
+}

modules/nf-core/regtools/junctionsextract/meta.yml

@@ -0,0 +1,55 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "regtools_junctionsextract"
+description: Extract exon-exon junctions from an RNAseq BAM file. The output is a
+  BED file in the BED12 format.
+keywords:
+  - regtools
+  - leafcutter
+  - RNA-seq
+  - splicing
+tools:
+  - "regtools":
+      description: "RegTools is a set of tools that integrate DNA-seq and RNA-seq data
+        to help interpret mutations in a regulatory and splicing context."
+      homepage: "https://regtools.readthedocs.io/en/latest/"
+      documentation: "https://regtools.readthedocs.io/en/latest/#usage"
+      tool_dev_url: "https://github.com/griffithlab/regtools"
+      licence: ["MIT"]
+      identifier: biotools:regtools
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.{bam}"
+    - bai:
+        type: file
+        description: Index to sorted BAM file
+        pattern: "*.{bai}"
+
+output:
+  - junc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.junc":
+          type: file
+          description: |
+            BED12 file containing exon-exon "regtools_junctionsextract"
+          pattern: "*.{junc}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@abartlett004"
+maintainers:
+  - "@abartlett004"

modules/nf-core/regtools/junctionsextract/tests/main.nf.test

@@ -0,0 +1,63 @@
+nextflow_process {
+
+    name "Test Process REGTOOLS_JUNCTIONSEXTRACT"
+    script "../main.nf"
+    process "REGTOOLS_JUNCTIONSEXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "regtools"
+    tag "regtools/junctionsextract"
+
+    test("homo_sapiens - bam-bai") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam-bai - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }
+            )
+        }
+
+    }
+
+}