diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 1f4d5a8..32705db 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -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-${{ steps.revision.outputs.revision }} + nextflow-config: | plugins { id 'nf-slack@0.5.0' id 'nf-schema@2.7.2' @@ -53,13 +57,23 @@ jobs: } parameters: | { - "outdir": "s3://${{ 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