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Update seqeralabs/action-tower-launch to v2 #2301

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Merged
adamrtalbot merged 6 commits into from
Jun 14, 2023
Merged

Update seqeralabs/action-tower-launch to v2 #2301

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8353340
Update seqeralabs/action-tower-launch to v1.2.4
adamrtalbot Jun 6, 2023
410db78
Update action to v2.0.0 (breaking change)
adamrtalbot Jun 6, 2023
e40580b
Reduce to shortened version of action-tower-launch version
adamrtalbot Jun 8, 2023
d24652a
Use specific Nextflow + nf-amazon version to get check if tests pass
adamrtalbot Jun 8, 2023
51882b2
Revert "Use specific Nextflow + nf-amazon version to get check if tes…
adamrtalbot Jun 9, 2023
7029b62
Merge branch 'dev' into update_action_tower_launch
adamrtalbot Jun 14, 2023
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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 @@ -12,6 +12,7 @@
- Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
- Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
- Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
- Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301))
- Remove schema validation from `lib` folder and use Nextflow [nf-validation plugin](https://nextflow-io.github.io/nf-validation/) instead ([#1771](https://github.com/nf-core/tools/pull/1771/))

### Download
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8 changes: 6 additions & 2 deletions nf_core/pipeline-template/.github/workflows/awsfulltest.yml
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Expand Up @@ -14,21 +14,25 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters {%- raw %}
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
parameters: |
{
"outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
}
profiles: test_full

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
8 changes: 6 additions & 2 deletions nf_core/pipeline-template/.github/workflows/awstest.yml
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Expand Up @@ -12,18 +12,22 @@ jobs:
steps:
# Launch workflow using Tower CLI tool action {%- raw %}
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
parameters: |
{
"outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
}
profiles: test

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json