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‎.github/CODEOWNERS

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@@ -13,3 +13,8 @@ modules/nf-core/preseq/ccurve/** @edmundmiller
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modules/nf-core/preseq/lcextrap/** @edmundmiller
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subworkflows/nf-core/homer/** @edmundmiller
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modules/nf-core/**/Dockerfile @edmundmiller @maxulysse
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subworkflows/nf-core/abundance_differential_filter/** @pinin4fjords
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subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/** @pinin4fjords
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modules/nf-core/deseq2 @pinin4fjords
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modules/nf-core/limma @pinin4fjords
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modules/nf-core/shinyngs @pinin4fjords

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

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@@ -17,7 +17,7 @@ inputs:
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runs:
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using: "composite"
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steps:
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- uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
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- uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
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with:
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distribution: "temurin"
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java-version: "17"
@@ -28,24 +28,16 @@ runs:
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version: "${{ env.NXF_VERSION }}"
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- name: Set up Python
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uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
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uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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with:
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python-version: "3.11"
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python-version: "3.13"
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- name: Set up nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: "${{ env.NFT_VER }}"
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install-pdiff: true
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- name: Install dependencies from universe repo
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if: contains(inputs.profile, 'singularity')
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shell: bash
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run: |
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sudo add-apt-repository universe
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sudo apt-get update
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sudo apt-get install -y uidmap squashfs-tools
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- name: Setup apptainer
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if: contains(inputs.profile, 'singularity')
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uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 #v2
@@ -81,9 +73,7 @@ runs:
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SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
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SENTIEON_AUTH_MECH: "GitHub Actions - token"
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run: |
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NFT_WORKDIR=~ \
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NFT_DIFF=pdiff \
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NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
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NFT_WORKDIR=~
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nf-test test \
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--profile=${{ inputs.profile }} \

‎.github/renovate.json5

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@@ -1,30 +1,26 @@
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{
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"$schema": "https://docs.renovatebot.com/renovate-schema.json",
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"extends": [
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$schema: "https://docs.renovatebot.com/renovate-schema.json",
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extends: [
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"github>nf-core/ops//.github/renovate/default.json5",
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"github>nf-core/ops//.github/renovate/process_updaters.json5"
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"github>nf-core/ops//.github/renovate/process_updaters.json5",
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],
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"prHeader": "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
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"packageRules": [
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prHeader: "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
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packageRules: [
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{
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"matchDatasources": [
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"conda",
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"pypi",
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"docker"
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matchDatasources: ["conda", "pypi", "docker"],
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automerge: false,
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},
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],
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customManagers: [
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{
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customType: "regex",
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managerFilePatterns: [
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"/(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$/",
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"/(^|/)action\\.ya?ml$/",
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],
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matchStrings: [
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"# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VER(SION)?\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s",
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],
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"automerge": false
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}
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},
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],
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"customManagers": [
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{
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"customType": "regex",
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"fileMatch": [
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"(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$",
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"(^|/)action\\.ya?ml$"
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],
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"matchStrings": [
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"# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VER(SION)?\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
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]
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}
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]
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}

‎.github/skip_nf_test.json

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@@ -18,7 +18,10 @@
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"modules/nf-core/cellranger/mkvdjref",
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"modules/nf-core/cellranger/multi",
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"modules/nf-core/cellranger/vdj",
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"modules/nf-core/cellrangerarc/mkref",
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"modules/nf-core/cellrangerarc/count",
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"modules/nf-core/cellrangerarc/mkgtf",
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"modules/nf-core/cellrangeratac/mkref",
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"modules/nf-core/checkqc",
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"modules/nf-core/coreograph",
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"modules/nf-core/custom/dumpsoftwareversions",
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"modules/nf-core/deepvariant/rundeepvariant",
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"modules/nf-core/deepvariant/vcfstatsreport",
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"modules/nf-core/doubletdetection",
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"modules/nf-core/ensemblvep/vep",
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"modules/nf-core/fastk/fastk",
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"modules/nf-core/fastk/histex",
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"modules/nf-core/fastk/merge",
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"modules/nf-core/ganon/table",
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"modules/nf-core/gatk4/cnnscorevariants",
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"modules/nf-core/gatk4/determinegermlinecontigploidy",
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"modules/nf-core/gatk4/unmarkduplicates",
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"modules/nf-core/genescopefk",
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"modules/nf-core/happy/sompy",
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"modules/nf-core/ilastik/multicut",
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"modules/nf-core/mitohifi/mitohifi",
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"modules/nf-core/mitohifi/findmitoreference",
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"modules/nf-core/molkartgarage/clahe",
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"modules/nf-core/ncbitools/vecscreen",
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"modules/nf-core/parabricks",
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"modules/nf-core/quartonotebook",
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"modules/nf-core/scimap/mcmicro",
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"modules/nf-core/spaceranger/mkref",
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"modules/nf-core/spotiflow",
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"modules/nf-core/svanalyzer/svbenchmark",
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"modules/nf-core/svtk/baftest",
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"modules/nf-core/svtk/rdtest2vcf",
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"modules/nf-core/svtk/standardize",
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"modules/nf-core/universc",
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"modules/nf-core/vt/decompose",
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"modules/nf-core/wittyer",
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"modules/nf-core/xeniumranger/resegment",
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"subworkflows/nf-core/bcl_demultiplex",
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"subworkflows/nf-core/deepvariant",
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"subworkflows/nf-core/fasta_clean_fcs",
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"subworkflows/nf-core/fasta_newick_epang_gappa",
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"subworkflows/nf-core/fastq_align_bamcmp_bwa",
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"subworkflows/nf-core/fastq_align_bwa",
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"subworkflows/nf-core/vcf_annotate_ensemblvep"
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"subworkflows/nf-core/fastq_align_bwa"
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],
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"docker": ["modules/nf-core/parabricks", "subworkflows/nf-core/deepvariant/tests/equality"],
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"singularity": [

‎.github/workflows/fix-linting.yml

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@@ -32,7 +32,7 @@ jobs:
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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35-
- uses: actions/setup-node@cdca7365b2dadb8aad0a33bc7601856ffabcc48e # v4
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- uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php

‎.github/workflows/lint.yml

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@@ -36,7 +36,7 @@ jobs:
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runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
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- uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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- uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
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with:
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extra_args: ""
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with:
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script: |
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return [...new Set(${{ steps.filter.outputs.modules_files }}
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.filter(x => x.endsWith('main.nf'))
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.map(path => path
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.replace('modules/nf-core/', '')
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.split('/')
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.slice(0, 2)
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.filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.md'))
93-
.join('/'))
91+
.replace(/\/main\.nf$/, '')
9492
)
95-
];
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)];
9694
- name: Get subworkflow name
9795
uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
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id: subworkflow_names
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with:
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script: |
10199
return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
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.filter(x => x.endsWith('main.nf'))
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.map(path => path
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.replace('subworkflows/nf-core/', '')
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.split('/')
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.slice(0, 2)
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.filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.md'))
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.join('/'))
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.replace(/\/main\.nf$/, '')
108104
)
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];
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)];
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- name: debug
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run: |
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- image=ubuntu22-full-x64
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name: nf-core lint modules
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needs: nf-core-changes
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if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }}
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if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
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strategy:
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fail-fast: false
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matrix:
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sudo rm -rf ./.* || true
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Set up Python
137-
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
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uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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with:
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python-version: "3.13"
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- name: Install pip
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- uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
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- uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
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with:
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distribution: "temurin"
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java-version: "17"
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name: nf-core lint subworkflows
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needs: nf-core-changes
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if: ${{ (needs.nf-core-changes.outputs.subworkflows == 'true') }}
169+
if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }}
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strategy:
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fail-fast: false
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matrix:
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sudo rm -rf ./.* || true
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Set up Python
185-
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
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uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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with:
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python-version: "3.13"
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‎.github/workflows/nf-test-gpu.yml

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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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with:
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fetch-depth: 0
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- name: test cuda
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run: |
113+
nvidia-smi -L
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- name: Run nf-test Action
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uses: ./.github/actions/nf-test-action
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env:
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confirm-pass-gpu:
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runs-on:
126129
- runs-on=${{ github.run_id }}-confirm-pass-gpu
127-
- runner=4cpu-linux-x64
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- runner=2cpu-linux-x64
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- image=ubuntu22-full-x64
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needs: [nf-test-gpu]
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if: always()

‎.github/workflows/pytest-workflow.yml

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tags: bwa/samse
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- profile: conda
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tags: cellpose
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- profile: conda
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tags: cellrangerarc/count
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- profile: conda
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tags: cellrangerarc/mkfastq
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- profile: conda
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tags: cellrangerarc/mkref
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- profile: conda
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tags: cellrangeratac/count
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- profile: conda
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tags: cellrangeratac/mkfastq
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- profile: conda
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tags: cellrangeratac/mkref
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- profile: conda
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tags: checkm2/databasedownload
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- profile: conda
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tags: happy/sompy
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- profile: conda
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tags: hlala/preparegraph
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- profile: conda
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tags: ilastik/pixelclassification
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- profile: conda
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tags: imputeme/vcftoprs
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- profile: conda
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tags: subworkflows/fasta_clean_fcs
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- profile: conda
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tags: svanalyzer/svbenchmark
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- profile: conda
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tags: svtk/standardize
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- profile: conda
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tags: universc
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- profile: singularity
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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244238
- name: Set up Python
245-
uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
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uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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with:
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python-version: "3.13"
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@@ -257,7 +251,7 @@ jobs:
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- name: Install Python dependencies
258252
run: python -m pip install --upgrade pip pytest-workflow cryptography
259253

260-
- uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
254+
- uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
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with:
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distribution: "temurin"
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java-version: "17"

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