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fix Download Pipeline Workflow #726

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merged 2 commits into from
Mar 28, 2024
Merged

fix Download Pipeline Workflow #726

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8a0f5f2
fix Download Pipeline Workflow
d4straub Mar 28, 2024
1c5ea7c
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d4straub Mar 28, 2024
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17 changes: 14 additions & 3 deletions .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 All @@ -28,7 +30,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
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' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --skip_qiime --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 --skip_qiime --outdir ./results
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#718](https://github.com/nf-core/ampliseq/pull/718) - Require a minimum sequence length of 50bp for taxonomic classifcation after using ITSx
- [#721](https://github.com/nf-core/ampliseq/pull/721) - Fix error `unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException` caused by a missing `\` in nf-core module `pigz/uncompress` (which had no consequences but was confusing)
- [#722](https://github.com/nf-core/ampliseq/pull/722) - When barrnap detects several genes select the lowest e-value
- [#726](https://github.com/nf-core/ampliseq/pull/726) - Add fallback to `download_pipeline.yml` because the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))

### `Dependencies`

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