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Use new nf-test features #6286
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Use new nf-test features #6286
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c2f20e4
ci: Attempt to split everything out
edmundmiller 8897f68
ci: Add changed since, sharding, and ci
edmundmiller 2e20ff4
ci: Add filter to try to get jobs split up
edmundmiller ea0de23
ci: Switch to only-changed
edmundmiller 2c5b4bd
ci: See if follow-dependencies works without "related-tests"
edmundmiller 6322086
ci: Remove skipped tests
edmundmiller 71d9e5a
ci: Actually use the nf-test version
edmundmiller afd049d
ci: module => process
edmundmiller a823ee3
ci: Clean up job names
edmundmiller 0d2c26c
dummy: Make a change
edmundmiller 97f6406
ci: Skip test.tap
edmundmiller c486922
ci: Add fetch-depth
edmundmiller d58ecdb
ci: Clean up name
edmundmiller 52a826d
ci: Lint everything
edmundmiller 1043d64
ci: Get the job names clean
edmundmiller 94c2453
ci: Add hide-progress on linting
edmundmiller ab5194b
ci: Add psuedocode for conda-fail.yml
edmundmiller 2a218e3
test: Snapshot the versions contents, not the hash
edmundmiller e833cd5
ci: Keep running nf-core lint the way it was
392ffe7
ci: Move conda skips out
edmundmiller af2d917
ci: Address a comment
edmundmiller 372625e
style: Move prettier and editorconfig to pre-commit
edmundmiller 1670c52
ci: Add note about nf-core lint pre-commit
edmundmiller adf6658
chore: Copy over conda skips
edmundmiller d0caf9e
ci: only-changed => changed-since
edmundmiller 3b97a33
Add confirm-pass
edmundmiller 865787a
ci: dynamically set shards
edmundmiller c141a14
ci: Run 3 process jobs per CI run as an example
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# TODO What do we do with these? | ||
# I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now | ||
# - 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/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/ensemblvep/vep | ||
# - profile: conda | ||
# path: modules/nf-core/fastk/fastk | ||
# - 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/mcquant | ||
# - 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: 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 |
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name: Run Linting | ||
on: | ||
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@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
- uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 | ||
- 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: "" | ||
|
||
################### | ||
# nf-core linting # | ||
################### | ||
# TODO Move these to pre-commit | ||
# https://github.com/nf-core/tools/pull/3141 | ||
nf-core-changes: | ||
name: nf-core-changes | ||
runs-on: ubuntu-latest | ||
outputs: | ||
tags: ${{ steps.filter.outputs.changes }} | ||
modules: ${{ steps.tags.outputs.modules }} | ||
subworkflows: ${{ steps.tags.outputs.subworkflows }} | ||
steps: | ||
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
with: | ||
fetch-depth: 2 # To retrieve the preceding commit. | ||
|
||
# TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | ||
- uses: mirpedrol/paths-filter@main | ||
id: filter | ||
with: | ||
filters: "tests/config/pytest_modules.yml" | ||
token: "" | ||
|
||
- name: Fetch module tags | ||
id: tags | ||
run: | | ||
echo modules=$(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-core-lint-modules: | ||
runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | ||
name: nf-core lint modules | ||
needs: nf-core-changes | ||
if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }} | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}" | ||
steps: | ||
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
|
||
- name: Set up Python | ||
uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | ||
with: | ||
python-version: "3.11" | ||
|
||
- uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # 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@b36c23c0d998641eff861008f374ee103c25ac73 # 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 subworkflows | ||
needs: nf-core-changes | ||
if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }} | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}" | ||
steps: | ||
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
|
||
- name: Set up Python | ||
uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | ||
with: | ||
python-version: "3.11" | ||
|
||
- name: Install pip | ||
run: python -m pip install --upgrade pip | ||
|
||
- uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # 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 }} | ||
|
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confirm-pass: | ||
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) }}" |
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This relies on the pytest_modules.yml tags, is that what you want?
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Nah, probably just want it to run on any module that's changed. We could include both the nf-test and pytest_modules ymls though I think.