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Add fallback to Download Pipeline Workflow #2846

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merged 3 commits into from
Mar 14, 2024
Merged

Add fallback to Download Pipeline Workflow #2846

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f066e65
Add fallback to DownloadPipeline-Workflow in case stub runs are not s…
MatthiasZepper Mar 13, 2024
393fd15
Changelog.
MatthiasZepper Mar 13, 2024
0a471a9
Need continue-on-error: true so that the job does not fail if the ste…
MatthiasZepper Mar 13, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
- Remove fasta default from nextflow.config ([#2828](https://github.com/nf-core/tools/pull/2828))
- Update templates to use nf-core/setup-nextflow v2
- Link to troubleshooting docs when pipeline fails ([#2845](https://github.com/nf-core/tools/pull/2845))
- Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))

### Linting

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15 changes: 13 additions & 2 deletions nf_core/pipeline-template/.github/workflows/download_pipeline.yml
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Expand Up @@ -14,6 +14,8 @@ on:
pull_request:
types:
- opened
- edited
- synchronize
branches:
- master
pull_request_target:
Expand Down Expand Up @@ -65,8 +67,17 @@ jobs:
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Run the downloaded pipeline
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
continue-on-error: true
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
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}
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