8000 fix Download Pipeline Workflow by Daniel-VM · Pull Request #123 · nf-core/bacass · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

fix Download Pipeline Workflow #123

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
Apr 2, 2024
Merged

fix Download Pipeline Workflow #123

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
cd0f061
fix download pipeline workflow - gitCLI
Daniel-VM Mar 30, 2024
1003eb3
fix linting error after updating workflow download pipeline
Daniel-VM Mar 30, 2024
c1ae590
update changelog #123
Daniel-VM Mar 30, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 13 additions & 2 deletions .github/workflows/download_pipeline.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
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
- 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
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#123](https://github.com/nf-core/bacass/pull/123) - Add fallback to `download_pipeline.yml` when the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))

### `Dependencies`

### `Deprecated`
Expand Down
0