Run Tests against real samples #15
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| 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 |