linting setup

.github/workflows/lint.yml

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+name: Run Linting
+on:
+  pull_request:
+    branches: [main, develop, release/*]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NXF_VER: "25.10.2"
+  NXF_SYNTAX_PARSER: "v2"
+
+jobs:
+  ###################
+  # nf-core linting #
+  ###################
+  nf-core-changes:
+    name: nf-core-changes
+    runs-on: ubuntu-latest
+
+    outputs:
+      # 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: ${{ steps.subworkflow_names.outputs.result }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
+
+      - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
+        id: filter
+        with:
+          filters: |
+            modules:
+              - added|modified: 'modules/UMCUGenetics/**'
+            subworkflows:
+              - added|modified: 'subworkflows/UMCUGenetics/**'
+          token: ""
+          list-files: "json"
+
+      - name: Get module name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: module_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.modules_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('modules/UMCUGenetics/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+      - name: Get subworkflow name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: subworkflow_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('subworkflows/UMCUGenetics/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+
+      - name: debug
+        run: |
+          echo ${{ steps.filter.outputs.modules_files }}
+          echo ${{ steps.module_names.outputs.result }}
+          echo ${{ steps.filter.outputs.subworkflows_files }}
+          echo ${{ steps.subworkflow_names.outputs.result }}
+
+  nf-core-lint-modules:
+    runs-on: ubuntu-latest
+    name: nf-core lint modules
+    needs: nf-core-changes
+    if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.14"
+
+      - uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
+        id: cache-pip
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+          restore-keys: |
+            ${{ runner.os }}-pip
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/UMCUGenetics/nf-core-tools.git
+
+      - 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_files != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.14"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/UMCUGenetics/nf-core-tools.git
+
+      - name: Lint subworkflow ${{ matrix.subworkflow }}
+        run: nf-core subworkflows lint ${{ matrix.subworkflow }}
+
+  confirm-pass-lint:
+    runs-on: ubuntu-latest
+    needs: [nf-core-lint-modules, nf-core-lint-subworkflows]
+    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: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

.nf-core.yml

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+org_path: UMCUGenetics
+repository_type: modules
+lint:
+  main_nf:
+    - when_exist
+    - test_main_tags
+    - container_links
+  module_tests:
+    - test_main_tags
+  meta_yml: false

README.md

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+# Modules
+
+
+## Repository Structure
+
+``` sh
+.
+├── README.md
+├── main.nf
+└── modules
+    └── UMCUGenetics
+```
+
+Modules are placed under the `./modules/UMCUGenetics/` folder in the format tool/subtool. For example `./modules/UMCUGenetics/samtools/view/`
+
+
+## Linting configuration
+Note: A fork of the nf-core CLI tools is used to run the linting actions (https://github.com/UMCUGenetics/nf-core-tools.git). This was done to make the linting of modules more customisable. For our purposes not all requirements by nf-core are neccesary.
+Linting configuration of this repository is configured in `.nf-core.yml` and is structured similarly to how `nf-core pipeline lint` configuration works (note that the tests in the yaml file are the ones being skipped, all the others are enabled). Usually, it is not neccessary to change this, but to view all available modules linting options:
+
+``` sh
+nf-core modules lint --list
+```
+
+Install the forked nf-core tools locally:
+
+``` sh
+pip install git+https://github.com/UMCUGenetics/nf-core-tools.git
+```
+
+### Github actions
+Linting is triggered automatically upon creating a pull request through a github actions workflow [.github/workflows/lint.yml]. The actions workflow is adapted from the actions workflow used in the [nf-core/modules](https://github.com/nf-core/modules) repository, with mostly small changes that remove nf-core specific action runners.
+
+### Running linting
+
+Alternatively, linting test can be manually executed:
+
+``` sh
+cd ./modules
+nf-core modules lint <tool/command>
+# Example: nf-core modules lint pgscatalog/combine
+```
+
+
+
+## Testing configuration
+TODO
+
+
+## Using a module in a nextflow pipeline
+Modules in this repository can be added to a pipeline similarly to how nf-core modules are installed.
+
+``` sh
+nf-core modules --git-remote https://github.com/UMCUGenetics/Modules install pgscatalog/combine
+```

main.nf

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+/*
+ * not actually used - just a placeholder
+ */

modules/UMCUGenetics/pgscatalog/combine/main.nf

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+process PGSCATALOG_COMBINE {
+    tag "${meta.id}"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pgscatalog-utils:1.4.4--pyhdfd78af_0'
+        : 'biocontainers/pgscatalog-utils:1.4.4--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(scoring_file)
+    val assembly_version
+
+    output:
+    tuple val(meta), path("*_normalised.txt.gz"), emit: normalised_model
+    path "versions.yml", emit: versions
+
+    script:
+    def prefix = task.ext.prefix ?: meta.id
+    """
+    pgscatalog-combine \\
+        -s ${scoring_file} \\
+        -t ${assembly_version} \\
+        -o ${prefix}_normalised.txt.gz
+
+
+    echo "pgscatalog-combine: 1.4.4" > versions.yml
+    """
+}

modules/UMCUGenetics/pgscatalog/combine/tests/main.nf.test

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+nextflow_process {
+    name "Test Process PGScatalog-combine"
+    script "../main.nf"
+    process "PGSCATALOG_COMBINE"
+
+    tag "modules/local"
+
+
+    test("Test Correct model formatting "){
+        when{
+            process{
+                """
+                input[0] = [[id: 'model'],
+                    file("${projectDir}/assets/models/BCAC_313_PRS_GRCh38.txt",
+                    checkifExists: true)]
+                input[1] = channel.value("GRCh38")
+                """
+            }
+
+            then {
+                assertAll(
+                    {assert process.success},
+                )
+            }
+        }
+    }
+}

modules/UMCUGenetics/pgscatalog/match/main.nf

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+process PGSCATALOG_MATCH {
+    tag "${meta.id}"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pgscatalog-utils:1.4.4--pyhdfd78af_0'
+        : 'biocontainers/pgscatalog-utils:1.4.4--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(pvar)
+    tuple val(meta2), path(scoring_file)
+
+
+    output:
+    tuple val(meta), path("*_summary.csv"), emit: summary
+    tuple val(meta), path("*.scorefile.gz"), emit: scorefile
+    tuple val(meta), path("*_log.csv.gz"), emit: log
+    path "versions.yml", emit: versions
+
+    script:
+    def prefix = task.ext.prefix ?: meta.id
+    def args = task.ext.args ?: ""
+    """
+    pgscatalog-match \\
+        ${args} \\
+        --dataset ${prefix} \\
+        --scorefiles ${scoring_file} \\
+        --target ${pvar} \\
+        --outdir ./
+
+    echo "pgscatalog-match: 1.4.4" > versions.yml
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "Cohort"
+    """
+	touch ${prefix}_summary.csv
+	touch ${prefix}.scorefile.gz
+    touch ${prefix}_log.csv.gz
+
+	echo "pgscatalog-match: 1.4.4" > versions.yml
+	"""
+}