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Pipeline template: Fix download test CI #2727

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merged 3 commits into from
Feb 6, 2024
Merged

Pipeline template: Fix download test CI #2727

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f3f7abc
Download CI Test: Set dev as the default branch and add customisation…
MatthiasZepper Feb 2, 2024
de73d39
Update Changelog.
MatthiasZepper Feb 2, 2024
90dd793
fix trailing whitespace
mashehu Feb 6, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
### Template

- Add empty line in README.md to fix badges. ([#2729](https://github.com/nf-core/tools/pull/2729))
- Replace automatic branch detection in `nf-core download` CI test with hardcoded `dev` and input. ([#2727](https://github.com/nf-core/tools/pull/2727))

### Linting

Expand Down Expand Up @@ -35,7 +36,7 @@

### Template

- Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download' ([#2618](https://github.com/nf-core/tools/pull/2618))
- Add a Github Action Workflow to the pipeline template that tests a successful download with `nf-core download` ([#2618](https://github.com/nf-core/tools/pull/2618))
- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
- Use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640))
- switch to new image syntax in readme ([#2645](https://github.com/nf-core/tools/pull/2645))
Expand Down
9 changes: 7 additions & 2 deletions nf_core/pipeline-template/.github/workflows/download_pipeline.yml
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Expand Up @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download'
# - 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
Expand Down Expand Up @@ -42,7 +47,7 @@ jobs:
run: |
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}

- name: Download the pipeline
env:
Expand All @@ -64,4 +69,4 @@ jobs:
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results {% endraw %}
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results{% endraw %}
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