prodTest.yml

name: "Run Tests against real samples"
on: [workflow_dispatch]
env:
  EMGB_KEGG_DB: "/vol/spool/toolkit/emgb/annotatedgenes2json_db_kegg-mirror-2022-12" 
  WORK_DIR: "/vol/spool/work"
  EMGB_DB_TITLES: "/vol/spool/toolkit/emgb/uniref90.titles.tsv.gz"
jobs:
  run_full_pipeline:
    timeout-minutes: 14400
    runs-on: [self-hosted, prodTest]
    steps:
      - uses: actions/checkout@v4
      - name: Set Secrets
        run: |
          make set_secrets SECRET_NAME=S3_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
          make set_secrets SECRET_NAME=S3_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
          make set_secrets SECRET_NAME=S3_kegg_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
          make set_secrets SECRET_NAME=S3_kegg_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
          make set_secrets SECRET_NAME=S3_EMGB_KEGG_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
          make set_secrets SECRET_NAME=S3_EMGB_KEGG_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
      - name: "Run full pipeline mode with all samples"
        run: |
          bash ./scripts/test_fullPipeline.sh \
          " -c /vol/spool/aws.config --databases=/vol/scratch/databases/  --logDir s3://toolkit-dev-benchmark \
           --steps.metabolomics.smetana.beforeProcessScript=/vol/spool/dockerPull.sh \
           --smetana_image=pbelmann/metabolomics:0.1.0 --steps.cooccurrence.beforeProcessScript=/vol/spool/dockerPull.sh \
           --steps.fragmentRecruitment.mashScreen.genomes=/vol/spool/toolkit/gtdb/paths.tsv \
           --steps.cooccurrence.inference.additionalParams.rscript=' --mincovthreshold 0.9 --maxzero 100 ' \
           --steps.annotation.mmseqs2.kegg.database.extractedDBPath='/vol/spool/toolkit/kegg-mirror-2021-01_mmseqs/sequenceDB' " \
          ./default/fullPipeline_illumina_nanpore.yml "" slurm || exit 1