AWS full test workflow revision handling differs from nf-core standard

[edmundmiller]

Description

The AWS test workflow in this repository uses different revision handling compared to the standard nf-core pattern, which may cause issues with S3 bucket path conflicts or unexpected behavior.

Current State (pairgenomealign)

revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pairgenomealign/work-${{ github.sha }}
parameters: |
  {
    "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pairgenomealign/results-test-${{ github.sha }}"
  }

Expected State (nf-core standard from rnaseq)

steps:
  - name: Set revision variable
    id: revision
    run: |
      echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"

  - name: Launch workflow via Seqera Platform
    with:
      revision: ${{ steps.revision.outputs.revision }}
      workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pairgenomealign/work-${{ steps.revision.outputs.revision }}
      parameters: |
        {
          "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pairgenomealign/results-${{ steps.revision.outputs.revision }}"
        }

Impact

The current hardcoded github.sha approach:

1. Doesn't follow the nf-core standard pattern used by other pipelines
2. May cause S3 path conflicts when the same SHA is used across different trigger events
3. Doesn't use the conventional 'dev' revision for non-release builds

Reference

Standard pattern implemented in: https://github.com/nf-core/rnaseq/blob/master/.github/workflows/awsfulltest.yml

Action Required

Update the workflow to use dynamic revision handling that sets revision to 'dev' for regular runs and github.sha only for workflow_dispatch and release events.

[charles-plessy]

Hi @edmundmiller can I ask you to look at #88 and tell me if the update to the 3.3.2 template is likely to fix the AWS pipeline run?