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Use matrix for all aws tests GHA #1212

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merged 4 commits into from
Sep 7, 2023
Merged

Use matrix for all aws tests GHA #1212

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a193d28
Use matrix for awstest github action
adamrtalbot Sep 6, 2023
09aaeb8
fixup
adamrtalbot Sep 6, 2023
031406a
more fixy
adamrtalbot Sep 6, 2023
ebd35c5
Update CHANGELOG.md
adamrtalbot Sep 7, 2023
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72 changes: 16 additions & 56 deletions .github/workflows/awstest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,79 +23,39 @@ on:
jobs:
trigger-profile-test:
name: Run AWS tests
if: ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.profiletest )
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
include:
- profile: test
enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.profiletest ) }}
- profile: test_full
enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.somatic ) }}
- profile: test_full_germline
enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline ) }}
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v2
if: ${{ matrix.enabled }}
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 }}/work/sarek/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
}
profiles: test
- uses: actions/upload-artifact@v3
with:
name: tower-profiletest-log
path: |
tower_action_*.log
tower_action_*.json

trigger-full-test-somatic:
name: Run AWS full tests
if: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.somatic ) }}
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
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 }}/work/sarek/work-${{ github.sha }}/somatic_test
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test"
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}/${{ matrix.profile }}"
}
profiles: test_full
profiles: ${{ matrix.profile }}

- uses: actions/upload-artifact@v3
if: ${{ matrix.enabled }}
with:
name: tower-full-somatic-log
name: tower-${{ matrix.profile }}-log
path: |
tower_action_*.log
tower_action_*.json

trigger-full-test-germline:
name: Run AWS full tests
if: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline ) }}
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
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 }}/work/sarek/work-${{ github.sha }}/germline_test
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test"
}
profiles: test_full_germline
- uses: actions/upload-artifact@v3
with:
name: tower-full-germline-log
path: tower_action_*.log
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -34,6 +34,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
- [#1180](https://github.com/nf-core/sarek/pull/1180) - Updating the nf-core modules
- [#1198](https://github.com/nf-core/sarek/pull/1198) - Prepare release `3.3.0`
- [#1200](https://github.com/nf-core/sarek/pull/1200) - Streamline Github Actions workflows
- [#1212](https://github.com/nf-core/sarek/pull/1212) - Use matrix for AWS megatests

### Fixed

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