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name: Test successful pipeline download with 'nf-core download'
# Run the workflow when:
# - dispatched manually
# - when a PR is opened or reopened to master branch
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
workflow_dispatch:
pull_request:
types:
- opened
branches:
- master
pull_request_target:
branches:
- master
env:
NXF_ANSI_LOG: false
jobs:
download:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
- uses: actions/setup-python@v5
with:
python-version: "3.11"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@v7
with:
singularity-version: 3.8.3
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install git+https://github.com/nf-core/tools.git@dev
- name: Get the repository name and current branch set as environment variable
run: |
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
run: |
nf-core download ${{ env.REPO_LOWERCASE }} \
--revision ${{ env.REPO_BRANCH }} \
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
--compress "none" \
--container-system 'singularity' \
--container-library "quay.io" -l "docker.io" -l "ghcr.io" \
--container-cache-utilisation 'amend' \
--download-configuration
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}
- name: Run the downloaded pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results