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Merged
MaximilianStammnitz merged 1 commit into from
Nov 12, 2026
Merged

Make AWS full tests use verified S3 inputs #105

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36 changes: 25 additions & 11 deletions .github/workflows/awsfulltest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,14 +23,18 @@ jobs:
echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"

- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
id: launch
uses: seqeralabs/action-seqera-launch@f7b1a39afc8bb65f58b84150cd214b33fe416fef
with:
workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
workspace-id: ${{ vars.TOWER_WORKSPACE_ID }}
access-token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute-env: ${{ vars.TOWER_COMPUTE_ENV }}
nextflow-version: 26.10.5
syntax-parser: v2
wait: completion
revision: ${{ steps.revision.outputs.revision }}
workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/deepmutscan/work-${{ steps.revision.outputs.revision }}
nextflow_config: |
work-dir: s3://${{ vars.AWS_S3_BUCKET }}/work/deepmutscan/work-${{ steps.revision.outputs.revision }}
nextflow-config: |
plugins {
id 'nf-slack@0.5.0'
id 'nf-schema@2.7.2'
Expand All @@ -53,13 +57,23 @@ jobs:
}
parameters: |
{
"outdir": "s3://${{ vars.AWS_S3_BUCKET }}/deepmutscan/results-${{ steps.revision.outputs.revision }}"
"outdir": "s3://${{ vars.AWS_S3_BUCKET }}/deepmutscan/results-${{ steps.revision.outputs.revision }}",
"input": "s3://${{ vars.AWS_S3_BUCKET }}/test-data/deepmutscan/PRJEB110196/GID1A_full.csv"
}
profiles: test_full

- name: Save Seqera Platform launch result
if: always() && steps.launch.outputs.workflow-id != ''
env:
SEQERA_WORKFLOW_ID: ${{ steps.launch.outputs.workflow-id }}
SEQERA_WORKFLOW_URL: ${{ steps.launch.outputs.workflow-url }}
SEQERA_WORKFLOW_STATUS: ${{ steps.launch.outputs.status }}
SEQERA_WORKFLOW_ERROR: ${{ steps.launch.outputs.error-message }}
run: |
jq -n '{workflowId: env.SEQERA_WORKFLOW_ID, workflowUrl: env.SEQERA_WORKFLOW_URL, status: env.SEQERA_WORKFLOW_STATUS, errorMessage: env.SEQERA_WORKFLOW_ERROR}' > seqera-launch.json

- uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
if: always() && steps.launch.outputs.workflow-id != ''
with:
name: Seqera Platform debug log file
path: |
tower_action_*.log
tower_action_*.json
name: Seqera Platform launch result
path: seqera-launch.json
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