forked from nf-core/omicsgenetraitassociation
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
22 changed files
with
403 additions
and
399 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| # Dockstore config version, not pipeline version | ||
| version: 1.2 | ||
| workflows: | ||
| - subclass: nfl | ||
| primaryDescriptorPath: /nextflow.config | ||
| publish: True | ||
| - subclass: nfl | ||
| primaryDescriptorPath: /nextflow.config | ||
| publish: True |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| contact_links: | ||
| - name: Join nf-core | ||
| url: https://nf-co.re/join | ||
| about: Please join the nf-core community here | ||
| - name: "Slack #omicsgenetraitassociation channel" | ||
| url: https://nfcore.slack.com/channels/omicsgenetraitassociation | ||
| about: Discussion about the nf-core/omicsgenetraitassociation pipeline | ||
| - name: Join nf-core | ||
| url: https://nf-co.re/join | ||
| about: Please join the nf-core community here | ||
| - name: "Slack #omicsgenetraitassociation channel" | ||
| url: https://nfcore.slack.com/channels/omicsgenetraitassociation | ||
| about: Discussion about the nf-core/omicsgenetraitassociation pipeline |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,42 +1,42 @@ | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
| push: | ||
| branches: | ||
| - dev | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| test: | ||
| name: Run pipeline with test data | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/omicsgenetraitassociation') }}" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
| test: | ||
| name: Run pipeline with test data | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/omicsgenetraitassociation') }}" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data | ||
| # For example: adding multiple test runs with different parameters | ||
| # Remember that you can parallelise this by using strategy.matrix | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| - name: Run pipeline with test data | ||
| # For example: adding multiple test runs with different parameters | ||
| # Remember that you can parallelise this by using strategy.matrix | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results |
Oops, something went wrong.