Fix mirtrace staging bug #1
Workflow file for this run
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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: | |
inputs: | |
testbranch: | |
description: "The specific branch you wish to utilize for the test execution of nf-core download." | |
required: true | |
default: "dev" | |
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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | |
with: | |
python-version: "3.11" | |
architecture: "x64" | |
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # 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.event.inputs.testbranch || 'dev' }}" >> ${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 |