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template: fix launch action #3827

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Merged
merged 3 commits into from
Oct 14, 2025
Merged

template: fix launch action #3827

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3f09a86
template: fix launch action
mashehu Oct 14, 2025
6afd4a9
[automated] Update CHANGELOG.md
nf-core-bot Oct 14, 2025
e2413b8
Update CHANGELOG.md
mashehu Oct 14, 2025
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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 @@ -15,6 +15,7 @@
- Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756))
- Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781))
- update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788))
- fix AWS tests launch action ([#3827](https://github.com/nf-core/tools/pull/3827))

### Linting

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12 changes: 6 additions & 6 deletions nf_core/pipeline-template/.github/workflows/awsfulltest.yml
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Expand Up @@ -28,21 +28,21 @@ jobs:
# 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
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
revision: ${{ steps.revision.outputs.revision }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %}
workdir: s3://${{ vars.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %}
parameters: |
{
"hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}",
"outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}"
"outdir": "s3://{% raw %}${{ vars.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}"
}
profiles: test_full

- uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: Seqera Platform debug log file
path: |
seqera_platform_action_*.log
seqera_platform_action_*.json
tower_action_*.log
tower_action_*.json
12 changes: 6 additions & 6 deletions nf_core/pipeline-template/.github/workflows/awstest.yml
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Expand Up @@ -14,20 +14,20 @@ jobs:
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
workdir: s3://${{ vars.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-${{ github.sha }}{% endraw %}"
"outdir": "s3://{% raw %}${{ vars.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
}
profiles: test

- uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: Seqera Platform debug log file
path: |
seqera_platform_action_*.log
seqera_platform_action_*.json
tower_action_*.log
tower_action_*.json