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Update CENTRIFUGE: bump versions, fix missing args, and command formatting #3923

Update CENTRIFUGE: bump versions, fix missing args, and command formatting

Update CENTRIFUGE: bump versions, fix missing args, and command formatting #3923

Workflow file for this run

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) }}"