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Update action tower launch to v2 #1135

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merged 8 commits into from
Dec 8, 2023
Merged

Update action tower launch to v2 #1135

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0156233
Update cloud_tests_full to action-tower-launch-v2
adamrtalbot Nov 27, 2023
5371d63
Update cloud_tests_small to action-tower-launch v2
adamrtalbot Nov 27, 2023
0a1d53a
Make output directory path instead of file?
adamrtalbot Nov 28, 2023
73fd071
Run on self-hosted
adamrtalbot Nov 28, 2023
d66151d
Revert self-hosted
adamrtalbot Nov 28, 2023
c958a01
Add revision parameter to action
adamrtalbot Nov 28, 2023
dbb185f
Update CHANGELOG.md
adamrtalbot Nov 28, 2023
a9f5810
Add PR to CHANGELOG
adamrtalbot Nov 28, 2023
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17 changes: 11 additions & 6 deletions .github/workflows/cloud_tests_full.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,9 @@ jobs:
matrix:
aligner: ["star_salmon", "star_rsem"]
steps:
- uses: seqeralabs/action-tower-launch@v1
- uses: seqeralabs/action-tower-launch@v2
with:
revision: ${{ github.sha }}
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
Expand All @@ -35,21 +36,23 @@ jobs:
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"aligner": "${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log

run-full-tests-on-gcp:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
runs-on: ubuntu-latest
strategy:
matrix:
aligner: ["star_salmon", "star_rsem"]
steps:
- uses: seqeralabs/action-tower-launch@v1
- uses: seqeralabs/action-tower-launch@v2
with:
revision: ${{ github.sha }}
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
Expand All @@ -60,21 +63,23 @@ jobs:
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"aligner": "${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log

run-full-tests-on-azure:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
runs-on: ubuntu-latest
strategy:
matrix:
aligner: ["star_salmon", "star_rsem"]
steps:
- uses: seqeralabs/action-tower-launch@v1
- uses: seqeralabs/action-tower-launch@v2
with:
revision: ${{ github.sha }}
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
Expand All @@ -85,7 +90,7 @@ jobs:
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"aligner": "${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
}
- uses: actions/upload-artifact@v3
Expand Down
6 changes: 3 additions & 3 deletions .github/workflows/cloud_tests_small.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ jobs:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
runs-on: ubuntu-latest
steps:
- 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 }}
Expand All @@ -38,7 +38,7 @@ jobs:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
runs-on: ubuntu-latest
steps:
- 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 }}
Expand All @@ -58,7 +58,7 @@ jobs:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
runs-on: ubuntu-latest
steps:
- 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 }}
Expand Down
2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling.

### Software dependencies

### Modules / Subworkflows
Expand Down
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