Fastq align dedup bwameth #17400
Workflow file for this run
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name: Run tests | ||
on: | ||
push: | ||
branches: | ||
# https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | ||
- "renovate/**" # branches Renovate creates | ||
pull_request: | ||
branches: [master] | ||
merge_group: | ||
types: [checks_requested] | ||
branches: [master] | ||
workflow_dispatch: | ||
inputs: | ||
runners: | ||
description: "Runners to test on" | ||
type: choice | ||
options: | ||
- "ubuntu-latest" | ||
- "self-hosted" | ||
default: "self-hosted" | ||
# 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 | ||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
jobs: | ||
pre-commit: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
with: | ||
python-version: "3.11" | ||
- uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | ||
# FIXME Flip this off once we get to less than a couple hundred. Adding | ||
# this so it will only run against changed files. It'll make it much | ||
# easier to fix these as they come up rather than everything at once. | ||
with: | ||
extra_args: "--all-files" | ||
prettier: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Check out repository | ||
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- name: Install NodeJS | ||
uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4 | ||
with: | ||
node-version: "20" | ||
- name: Install Prettier | ||
run: npm install -g [email protected] | ||
- name: Run Prettier --check | ||
run: prettier --check . | ||
editorconfig: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4 | ||
with: | ||
node-version: "20" | ||
- name: Install editorconfig-checker | ||
run: npm install -g editorconfig-checker | ||
- name: Run ECLint check | ||
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | ||
pytest-changes: | ||
name: pytest-changes | ||
runs-on: ubuntu-latest | ||
outputs: | ||
tags: ${{ steps.filter.outputs.changes }} | ||
modules: ${{ steps.tags.outputs.modules }} | ||
subworkflows: ${{ steps.tags.outputs.subworkflows }} | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
with: | ||
fetch-depth: 2 # To retrieve the preceding commit. | ||
- uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | ||
id: filter | ||
with: | ||
filters: "tests/config/pytest_modules.yml" | ||
token: "" | ||
- name: Fetch module tags | ||
id: tags | ||
run: | | ||
echo modules=$(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: debug | ||
run: | | ||
echo ${{ steps.tags.outputs.modules }} | ||
echo ${{ steps.tags.outputs.subworkflows }} | ||
nf-test-changes: | ||
name: nf-test-changes | ||
runs-on: ubuntu-latest | ||
outputs: | ||
# Expose detected tags as 'modules' and 'workflows' output variables | ||
paths: ${{ steps.list.outputs.components }} | ||
modules: ${{ steps.outputs.outputs.modules }} | ||
subworkflows: ${{ steps.outputs.outputs.subworkflows}} | ||
# Prod for version bumping | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
with: | ||
fetch-depth: 0 | ||
- name: List nf-test files | ||
id: list | ||
uses: adamrtalbot/detect-nf-test-changes@7c8be3ffd0d6538312b363c8c949dbbf5f26c3dd # v0.0.4 | ||
with: | ||
head: ${{ github.sha }} | ||
base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} | ||
n_parents: 2 | ||
- name: Separate modules and subworkflows | ||
id: outputs | ||
run: | | ||
echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT | ||
echo subworkflows=$(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.modules }} | ||
echo ${{ steps.outputs.outputs.subworkflows }} | ||
nf-core-lint-modules: | ||
runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }} | ||
name: nf-core-lint-modules | ||
needs: [pytest-changes, nf-test-changes] | ||
if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }} | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
tags: | ||
[ | ||
"${{ fromJson(needs.pytest-changes.outputs.modules) }}", | ||
"${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | ||
] | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- name: Set up Python | ||
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
with: | ||
python-version: "3.11" | ||
- uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4 | ||
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@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | ||
with: | ||
distribution: "temurin" | ||
java-version: "17" | ||
- name: Setup 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/nf-core/tools.git@dev | ||
- name: Lint module ${{ matrix.tags }} | ||
run: nf-core modules lint ${{ matrix.tags }} | ||
nf-core-lint-subworkflows: | ||
runs-on: ubuntu-latest | ||
name: nf-core-lint-modules | ||
needs: [pytest-changes, nf-test-changes] | ||
if: ${{ (needs.pytest-changes.outputs.subworkflows != '[]') || ( needs.nf-test-changes.outputs.subworkflows != '[]') }} | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
tags: | ||
[ | ||
"${{ fromJson(needs.pytest-changes.outputs.subworkflows) }}", | ||
"${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}", | ||
] | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- name: Set up Python | ||
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
with: | ||
python-version: "3.11" | ||
- name: Install pip | ||
run: python -m pip install --upgrade pip | ||
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | ||
with: | ||
distribution: "temurin" | ||
java-version: "17" | ||
- name: Setup Nextflow | ||
uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 | ||
- 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 }} | ||
pytest: | ||
runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }} | ||
name: pytest | ||
needs: [pytest-changes] | ||
if: needs.pytest-changes.outputs.tags != '[]' | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] | ||
profile: [conda, docker, singularity] | ||
exclude: | ||
- tags: nf-test | ||
- profile: conda | ||
tags: backsub | ||
- profile: conda | ||
tags: bases2fastq | ||
- profile: singularity | ||
tags: bases2fastq | ||
- profile: conda | ||
tags: basicpy | ||
- profile: conda | ||
tags: bcl2fastq | ||
- profile: conda | ||
tags: bclconvert | ||
- profile: conda | ||
tags: bwa/aln | ||
- profile: conda | ||
tags: bwa/index | ||
- profile: conda | ||
tags: bwa/mem | ||
- profile: conda | ||
tags: bwa/sampe | ||
- profile: conda | ||
tags: bwa/samse | ||
- profile: conda | ||
tags: cellpose | ||
- profile: conda | ||
tags: cellrangerarc/count | ||
- profile: conda | ||
tags: cellrangerarc/mkfastq | ||
- profile: conda | ||
tags: cellrangerarc/mkref | ||
- profile: conda | ||
tags: cellrangeratac/count | ||
- profile: conda | ||
tags: cellrangeratac/mkfastq | ||
- profile: conda | ||
tags: cellrangeratac/mkref | ||
- profile: conda | ||
tags: checkm2/databasedownload | ||
- profile: conda | ||
tags: checkm2/predict | ||
- profile: conda | ||
tags: controlfreec/makegraph2 | ||
- profile: conda | ||
tags: coreograph | ||
- profile: conda | ||
tags: deepcell/mesmer | ||
- profile: conda | ||
tags: deepvariant | ||
- profile: conda | ||
tags: fastani | ||
- profile: conda | ||
tags: fastk/fastk | ||
- profile: conda | ||
tags: fastk/histex | ||
- profile: conda | ||
tags: fastk/merge | ||
- profile: conda | ||
tags: fcs/fcsadaptor | ||
- profile: conda | ||
tags: fcs/fcsgx | ||
- profile: conda | ||
tags: gatk4/cnnscorevariants | ||
- profile: conda | ||
tags: gatk4/determinegermlinecontigploidy | ||
- profile: singularity | ||
tags: gatk4/determinegermlinecontigploidy | ||
- profile: conda | ||
tags: gatk4/germlinecnvcaller | ||
- profile: conda | ||
tags: gatk4/postprocessgermlinecnvcalls | ||
- profile: conda | ||
tags: genescopefk | ||
- profile: conda | ||
tags: happy/sompy | ||
- profile: conda | ||
tags: hlala/preparegraph | ||
- profile: conda | ||
tags: ilastik/multicut | ||
- profile: conda | ||
tags: ilastik/pixelclassification | ||
- profile: conda | ||
tags: imputeme/vcftoprs | ||
- profile: conda | ||
tags: islandpath | ||
- profile: conda | ||
tags: manta/convertinversion | ||
- profile: conda | ||
tags: mcstaging/imc2mc | ||
- profile: conda | ||
tags: mcquant | ||
- profile: conda | ||
tags: medaka | ||
- profile: conda | ||
tags: merquryfk/katcomp | ||
- profile: conda | ||
tags: merquryfk/katgc | ||
- profile: conda | ||
tags: merquryfk/merquryfk | ||
- profile: conda | ||
tags: merquryfk/ploidyplot | ||
- profile: conda | ||
tags: minimap2/align | ||
- profile: conda | ||
tags: mitohifi/findmitoreference | ||
- profile: conda | ||
tags: mitohifi/mitohifi | ||
- profile: conda | ||
tags: nanoplot | ||
- profile: conda | ||
tags: ncbitools/vecscreen | ||
- profile: conda | ||
tags: parabricks/dbsnp | ||
- profile: conda | ||
tags: parabricks/deepvariant | ||
- profile: conda | ||
tags: parabricks/genotypegvcf | ||
- profile: conda | ||
tags: parabricks/haplotypecaller | ||
- profile: conda | ||
tags: parabricks/indexgvcf | ||
- profile: conda | ||
tags: parabricks/mutectcaller | ||
- profile: conda | ||
tags: picard/collecthsmetrics | ||
- profile: conda | ||
tags: picard/collectwgsmetrics | ||
- profile: conda | ||
tags: sentieon/applyvarcal | ||
- profile: conda | ||
tags: sentieon/datametrics | ||
- profile: conda | ||
tags: sentieon/dnamodelapply | ||
- profile: conda | ||
tags: sentieon/dnascope | ||
- profile: conda | ||
tags: sentieon/readwriter | ||
- profile: conda | ||
tags: sentieon/tnfilter | ||
- profile: conda | ||
tags: sentieon/tnhaplotyper2 | ||
- profile: conda | ||
tags: sentieon/tnscope | ||
- profile: conda | ||
tags: sentieon/varcal | ||
- profile: conda | ||
tags: sentieon/wgsmetrics | ||
- profile: conda | ||
tags: subworkflows/bam_qc_picard | ||
- profile: conda | ||
tags: subworkflows/bcl_demultiplex | ||
- profile: conda | ||
tags: subworkflows/fasta_clean_fcs | ||
- profile: conda | ||
tags: svanalyzer/svbenchmark | ||
- profile: conda | ||
tags: universc | ||
- profile: singularity | ||
tags: universc | ||
- profile: conda | ||
tags: vt/decompose | ||
env: | ||
NXF_ANSI_LOG: false | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- name: Set up Python | ||
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
with: | ||
python-version: "3.11" | ||
- uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4 | ||
id: cache-pip-pytest | ||
with: | ||
path: ~/.cache/pip | ||
key: ${{ runner.os }}-pip-pytest | ||
restore-keys: | | ||
${{ runner.os }}-pip-pytest | ||
- name: Install Python dependencies | ||
run: python -m pip install --upgrade pip pytest-workflow cryptography | ||
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | ||
with: | ||
distribution: "temurin" | ||
java-version: "17" | ||
- name: Setup Nextflow ${{ matrix.NXF_VER }} | ||
uses: nf-core/setup-nextflow@v2 | ||
with: | ||
version: "${{ matrix.NXF_VER }}" | ||
- name: Setup apptainer | ||
if: matrix.profile == 'singularity' | ||
uses: eWaterCycle/setup-apptainer@main | ||
- name: Set up Singularity | ||
if: matrix.profile == 'singularity' | ||
run: | | ||
mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
- name: Set up miniconda | ||
uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 | ||
with: | ||
miniconda-version: "latest" | ||
channels: conda-forge,bioconda | ||
python-version: ${{ matrix.python-version }} | ||
conda-remove-defaults: true | ||
- name: Conda setup | ||
run: | | ||
conda clean -a | ||
conda install -n base conda-libmamba-solver | ||
conda config --set solver libmamba | ||
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | ||
echo $(realpath python) >> $GITHUB_PATH | ||
# Test the module | ||
- name: Run pytest-workflow | ||
# only use one thread for pytest-workflow to avoid race condition on conda cache. | ||
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | ||
- name: Output log on failure | ||
if: failure() | ||
run: | | ||
sudo apt-get update > /dev/null | ||
sudo apt-get install bat > /dev/null | ||
batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err} | ||
- name: Setting global variables | ||
uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 | ||
id: parsed | ||
with: | ||
script: | | ||
return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') | ||
result-encoding: string | ||
- name: Upload logs on failure | ||
if: failure() | ||
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | ||
with: | ||
name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} | ||
path: | | ||
/home/ubuntu/pytest_workflow_*/*/.nextflow.log | ||
/home/ubuntu/pytest_workflow_*/*/log.out | ||
/home/ubuntu/pytest_workflow_*/*/log.err | ||
/home/ubuntu/pytest_workflow_*/*/work | ||
!/home/ubuntu/pytest_workflow_*/*/work/conda | ||
!/home/ubuntu/pytest_workflow_*/*/work/singularity | ||
!${{ github.workspace }}/.singularity | ||
nf-test: | ||
runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | ||
name: nf-test | ||
needs: [nf-test-changes] | ||
if: ( needs.nf-test-changes.outputs.paths != '[]' ) | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"] | ||
profile: [conda, docker_self_hosted, singularity] | ||
exclude: | ||
- path: modules/nf-core/nf-test | ||
- profile: conda | ||
path: modules/nf-core/angsd/gl | ||
- profile: conda | ||
path: modules/nf-core/annotsv/installannotations | ||
- profile: conda | ||
path: modules/nf-core/happy/sompy | ||
- profile: conda | ||
path: modules/nf-core/backsub | ||
- profile: conda | ||
path: modules/nf-core/bakta/bakta | ||
- profile: conda | ||
path: modules/nf-core/bakta/baktadbdownload | ||
- profile: conda | ||
path: modules/nf-core/bases2fastq | ||
- profile: conda | ||
path: modules/nf-core/bcl2fastq | ||
- profile: conda | ||
path: modules/nf-core/bclconvert | ||
- profile: conda | ||
path: modules/nf-core/celesta | ||
- profile: conda | ||
path: modules/nf-core/cellpose | ||
- profile: conda | ||
path: modules/nf-core/cellranger/count | ||
- profile: conda | ||
path: modules/nf-core/cellranger/mkfastq | ||
- profile: conda | ||
path: modules/nf-core/cellranger/mkgtf | ||
- profile: conda | ||
path: modules/nf-core/cellranger/mkref | ||
- profile: conda | ||
path: modules/nf-core/cellranger/mkvdjref | ||
- profile: conda | ||
path: modules/nf-core/cellranger/multi | ||
- profile: conda | ||
path: modules/nf-core/cellranger/vdj | ||
- profile: conda | ||
path: modules/nf-core/checkqc | ||
- profile: conda | ||
path: modules/nf-core/custom/dumpsoftwareversions | ||
- profile: conda | ||
path: modules/nf-core/deepcell/mesmer | ||
- profile: conda | ||
path: modules/nf-core/deepsomatic | ||
- profile: singularity | ||
path: modules/nf-core/deepsomatic | ||
- profile: conda | ||
path: modules/nf-core/deepvariant | ||
- profile: conda | ||
path: modules/nf-core/deepvariant/callvariants | ||
- profile: conda | ||
path: modules/nf-core/deepvariant/makeexamples | ||
- profile: conda | ||
path: modules/nf-core/deepvariant/postprocessvariants | ||
- profile: conda | ||
path: modules/nf-core/deepvariant/rundeepvariant | ||
- profile: conda | ||
path: modules/nf-core/deepvariant/vcfstatsreport | ||
- profile: conda | ||
path: modules/nf-core/doubletdetection | ||
- profile: conda | ||
path: modules/nf-core/ensemblvep/vep | ||
- profile: conda | ||
path: modules/nf-core/fastk/fastk | ||
- profile: conda | ||
path: modules/nf-core/cellrangerarc/mkgtf | ||
- profile: conda | ||
path: modules/nf-core/fastk/histex | ||
- profile: conda | ||
path: modules/nf-core/fastk/merge | ||
- profile: conda | ||
path: modules/nf-core/fcs/fcsadaptor | ||
- profile: conda | ||
path: modules/nf-core/fcs/fcsgx | ||
- profile: conda | ||
path: modules/nf-core/ganon/buildcustom | ||
- profile: conda | ||
path: modules/nf-core/ganon/classify | ||
- profile: conda | ||
path: modules/nf-core/ganon/report | ||
- profile: conda | ||
path: modules/nf-core/ganon/table | ||
- profile: conda | ||
path: modules/nf-core/gatk4/cnnscorevariants | ||
- profile: conda | ||
path: modules/nf-core/gatk4/determinegermlinecontigploidy | ||
- profile: conda | ||
path: modules/nf-core/genescopefk | ||
- profile: conda | ||
path: modules/nf-core/ilastik/multicut | ||
- profile: conda | ||
path: modules/nf-core/ilastik/pixelclassification | ||
- profile: conda | ||
path: modules/nf-core/imputeme/vcftoprs | ||
- profile: conda | ||
path: modules/nf-core/mcstaging/imc2mc | ||
- profile: conda | ||
path: modules/nf-core/mcquant | ||
- profile: conda | ||
path: modules/nf-core/mcstaging/phenoimager2mc | ||
- profile: conda | ||
path: modules/nf-core/merquryfk/katcomp | ||
- profile: conda | ||
path: modules/nf-core/merquryfk/katgc | ||
- profile: conda | ||
path: modules/nf-core/merquryfk/merquryfk | ||
- profile: conda | ||
path: modules/nf-core/merquryfk/ploidyplot | ||
- profile: conda | ||
path: modules/nf-core/molkartgarage/clahe | ||
- profile: conda | ||
path: modules/nf-core/quartonotebook | ||
- profile: conda | ||
path: modules/nf-core/scimap/spatiallda | ||
- profile: conda | ||
path: modules/nf-core/sentieon/bwaindex | ||
- profile: conda | ||
path: modules/nf-core/sentieon/bwamem | ||
- profile: conda | ||
path: modules/nf-core/sentieon/datametrics | ||
- profile: conda | ||
path: modules/nf-core/sentieon/dedup | ||
- profile: conda | ||
path: modules/nf-core/sentieon/qualcal | ||
- profile: conda | ||
path: modules/nf-core/spaceranger/mkgtf | ||
- profile: conda | ||
path: modules/nf-core/spaceranger/mkref | ||
- profile: conda | ||
path: modules/nf-core/spaceranger/count | ||
- profile: conda | ||
path: modules/nf-core/spotiflow | ||
- profile: conda | ||
path: modules/nf-core/svanalyzer/svbenchmark | ||
- profile: conda | ||
path: modules/nf-core/universc | ||
- profile: singularity | ||
path: modules/nf-core/universc | ||
- profile: conda | ||
path: modules/nf-core/vt/decompose | ||
- profile: singularity | ||
path: modules/nf-core/bases2fastq | ||
- profile: conda | ||
path: modules/nf-core/wittyer | ||
- profile: conda | ||
path: modules/nf-core/islandpath | ||
- profile: conda | ||
path: modules/nf-core/scimap/mcmicro | ||
- profile: conda | ||
path: subworkflows/nf-core/vcf_annotate_ensemblvep | ||
- profile: conda | ||
path: subworkflows/nf-core/bcl_demultiplex | ||
- profile: conda | ||
path: subworkflows/nf-core/deepvariant | ||
- profile: conda | ||
path: subworkflows/nf-core/fastq_align_bamcmp_bwa | ||
- profile: conda | ||
path: subworkflows/nf-core/fastq_align_bwa | ||
- profile: conda | ||
path: subworkflows/nf-core/fasta_newick_epang_gappa | ||
- path: modules/nf-core/parabricks/fq2bammeth | ||
- path: modules/nf-core/parabricks/fq2bam | ||
- path: modules/nf-core/parabricks/applybqsr | ||
- profile: conda | ||
path: modules/nf-core/xeniumranger/relabel | ||
- profile: conda | ||
path: modules/nf-core/xeniumranger/rename | ||
- profile: conda | ||
path: modules/nf-core/xeniumranger/resegment | ||
- profile: conda | ||
path: modules/nf-core/xeniumranger/import-segmentation | ||
- profile: [conda, docker_self_hosted, singularity] | ||
path: subworkflows/nf-core/fastq_align_dedup_bwameth/gpu.nf.test | ||
env: | ||
NXF_ANSI_LOG: false | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
- name: Run nf-test Action | ||
uses: ./.github/actions/nf-test-action | ||
with: | ||
path: ${{ matrix.path }} | ||
profile: ${{ matrix.profile }} | ||
nf-test-gpu: | ||
runs-on: "gpu" | ||
name: nf-test-gpu | ||
needs: [nf-test-changes] | ||
if: ( needs.nf-test-changes.outputs.paths != '[]' && contains(needs.nf-test-changes.outputs.paths, 'modules/nf-core/parabricks', 'subworkflows/nf-core/fastq_align_dedup_bwameth') ) | ||
Check failure on line 692 in .github/workflows/test.yml GitHub Actions / Run testsInvalid workflow file
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||
strategy: | ||
fail-fast: false | ||
matrix: | ||
include: | ||
- path: modules/nf-core/parabricks/applybqsr | ||
profile: [docker_self_hosted, singularity] | ||
- path: modules/nf-core/parabricks/fq2bam | ||
profile: [docker_self_hosted, singularity] | ||
- path: modules/nf-core/parabricks/fq2bammeth | ||
profile: [docker_self_hosted, singularity] | ||
- path: subworkflows/nf-core/fastq_align_dedup_bwameth/gpu.nf.test | ||
profile: [docker_self_hosted, singularity] | ||
env: | ||
NXF_ANSI_LOG: false | ||
steps: | ||
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
- name: Run nf-test Action | ||
uses: ./.github/actions/nf-test-action | ||
env: | ||
SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | ||
SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | ||
SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | ||
SENTIEON_AUTH_MECH: "GitHub Actions - token" | ||
with: | ||
path: ${{ matrix.path }} | ||
profile: ${{ matrix.profile }},gpu | ||
confirm-pass: | ||
runs-on: ubuntu-latest | ||
needs: | ||
[ | ||
prettier, | ||
editorconfig, | ||
pytest-changes, | ||
nf-core-lint-modules, | ||
nf-core-lint-subworkflows, | ||
pytest, | ||
nf-test-changes, | ||
nf-test, | ||
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: debug-print | ||
if: always() | ||
run: | | ||
echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |