Skip to content

Patched 183,184,179,178 for 2.2.1 #16

Patched 183,184,179,178 for 2.2.1

Patched 183,184,179,178 for 2.2.1 #16

name: Test successful pipeline download with 'nf-core pipelines download'
# Run the workflow when:
# - dispatched manually
# - when a PR is opened or reopened to main 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:
inputs:
testbranch:
description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
required: true
default: "dev"
pull_request:
types:
- opened
- edited
- synchronize
branches:
- main
pull_request_target:
branches:
- main
env:
NXF_ANSI_LOG: false
jobs:
download:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.12"
architecture: "x64"
- name: Setup Apptainer
uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
with:
apptainer-version: 1.3.4
- 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.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
- name: Make a cache directory for the container images
run: |
mkdir -p ./singularity_container_images
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
run: |
nf-core pipelines 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 "community.wave.seqera.io" \
--container-cache-utilisation 'amend' \
--download-configuration 'yes'
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}
- name: Count the downloaded number of container images
id: count_initial
run: |
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
echo "Initial container image count: $image_count"
echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
continue-on-error: true
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
- name: Count the downloaded number of container images
id: count_afterwards
run: |
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
echo "Post-pipeline run container image count: $image_count"
echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
- name: Compare container image counts
run: |
if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
initial_count=${{ env.IMAGE_COUNT_INITIAL }}
final_count=${{ env.IMAGE_COUNT_AFTER }}
difference=$((final_count - initial_count))
echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
tree ./singularity_container_images
exit 1
else
echo "The pipeline can be downloaded successfully!"
fi