Update CENTRIFUGE: bump versions, fix missing args, and command formatting #3923
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name: Run nf-test | |
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: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
NFT_VER: "0.9.2" | |
NXF_ANSI_LOG: false | |
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
NXF_VER: "24.10.2" | |
jobs: | |
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: | |
- name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner | |
run: | | |
ls -la ./ | |
rm -rf ./* || true | |
rm -rf ./.??* || true | |
ls -la ./ | |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
with: | |
fetch-depth: 0 | |
- name: List nf-test files | |
id: list | |
uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6 | |
with: | |
head: ${{ github.sha }} | |
base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} | |
n_parents: 0 | |
exclude_tags: "gpu" | |
- name: Separate modules and subworkflows | |
id: outputs | |
run: | | |
echo modules=$(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.list.outputs.components }} | |
echo ${{ steps.outputs.outputs.modules }} | |
echo ${{ steps.outputs.outputs.subworkflows }} | |
nf-test: | |
runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }}" | |
needs: nf-test-changes | |
if: ${{ needs.nf-test-changes.outputs.modules != '[]' || needs.nf-test-changes.outputs.subworkflows != '[]' }} | |
strategy: | |
fail-fast: false | |
matrix: | |
shard: [1, 2, 3, 4, 5] | |
profile: [conda, docker_self_hosted, singularity] | |
env: | |
NXF_ANSI_LOG: false | |
TOTAL_SHARDS: 5 | |
steps: | |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
with: | |
fetch-depth: 0 | |
- 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: | |
profile: ${{ matrix.profile }} | |
shard: ${{ matrix.shard }} | |
total_shards: ${{ env.TOTAL_SHARDS }} | |
paths: "${{ join(fromJson(needs.nf-test-changes.outputs.paths), ' ') }}" | |
confirm-pass: | |
runs-on: ubuntu-latest | |
needs: [nf-test] | |
if: always() | |
steps: | |
- name: One or more tests failed | |
if: ${{ contains(needs.*.result, 'failure') }} | |
run: exit 1 | |
- name: One or more tests cancelled | |
if: ${{ contains(needs.*.result, 'cancelled') }} | |
run: exit 1 | |
- name: All tests ok | |
if: ${{ contains(needs.*.result, 'success') }} | |
run: exit 0 | |
- name: debug-print | |
if: always() | |
run: | | |
echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |