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Add umicollapse as an alternative to umi-tools #3181

Add umicollapse as an alternative to umi-tools

Add umicollapse as an alternative to umi-tools #3181

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
pull_request:
release:
types: [published]
workflow_dispatch:
env:
NFT_DIFF: "pdiff"
NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
NFT_VER: "0.9.0"
NFT_WORKDIR: "~"
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
nf-test-changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
nf_test_files: ${{ steps.list.outputs.components }}
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: List nf-test files
id: list
uses: adamrtalbot/[email protected]
with:
head: ${{ github.sha }}
base: origin/${{ github.base_ref }}
include: .github/include.yaml
- name: print list of nf-test files
run: |
echo ${{ steps.list.outputs.components }}
test:
name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})"
needs: [nf-test-changes]
if: needs.nf-test-changes.outputs.nf_test_files != '[]'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
profile:
- "docker"
- "singularity"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
exclude:
- isMaster: false
profile: "singularity"
- NXF_VER: "latest-everything"
profile: "singularity"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
with:
distribution: "temurin"
java-version: "17"
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Set up 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: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: ${{ env.NFT_VER }}
- uses: actions/setup-python@v4
with:
python-version: "3.11"
architecture: "x64"
- name: Install pdiff to see diff between nf-test snapshots
run: |
python -m pip install --upgrade pip
pip install pdiff
- name: Clean up Disk space
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run nf-test
run: |
nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: test.xml
confirm-pass:
runs-on: ubuntu-latest
needs: [test]
if: always()
steps:
- name: All tests ok
if: ${{ !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) }}"