                                                                                
 Usage: dyec workflow launch [OPTIONS]                                          
                                                                                
 Launch daylily-omics-analysis inside tmux on the headnode.                     
                                                                                
╭─ Options ────────────────────────────────────────────────────────────────────╮
│    --profile                                    TEXT     AWS CLI profile.    │
│    --region                                     TEXT     AWS region.         │
│    --cluster,--clust…                           TEXT     ParallelCluster     │
│                                                          name.               │
│    --stage-dir                                  TEXT     Specific staging    │
│                                                          directory           │
│                                                          containing          │
│                                                          generated           │
│                                                          manifests.          │
│    --run-context-file                           PATH     Local runs.tsv file │
│                                                          to copy to          │
│                                                          config/runs.tsv for │
│                                                          run-analysis        │
│                                                          workflows.          │
│    --samples-file                               PATH     Local samples.tsv   │
│                                                          file to copy to     │
│                                                          config/samples.tsv  │
│                                                          for sample-analysis │
│                                                          workflows.          │
│    --units-file                                 PATH     Local units.tsv     │
│                                                          file to copy to     │
│                                                          config/units.tsv    │
│                                                          for sample-analysis │
│                                                          workflows.          │
│    --stage-base                                 TEXT     Base staging        │
│                                                          directory to scan   │
│                                                          when --stage-dir is │
│                                                          omitted.            │
│                                                          [default:           │
│                                                          /fsx/staging/stage… │
│    --input-staging         --no-input-stagi…             Copy staged         │
│                                                          samples/units into  │
│                                                          the workflow clone. │
│                                                          [default:           │
│                                                          input-staging]      │
│    --default-activat…      --no-default-act…             Run the standard    │
│                                                          dyoainit plus Slurm │
│                                                          day_activate setup  │
│                                                          before              │
│                                                          --dy-command.       │
│                                                          [default:           │
│                                                          default-activation] │
│    --bootstrap-test-…                                    Copy DayOA bundled  │
│                                                          test samples and    │
│                                                          units into config/  │
│                                                          before launch.      │
│    --session-name                               TEXT     Tmux session name.  │
│                                                          Defaults to         │
│                                                          --analysis-id.      │
│ *  --analysis-id                                TEXT     Required analysis   │
│                                                          identifier used for │
│                                                          the FSx analysis    │
│                                                          directory.          │
│                                                          [required]          │
│    --executing-entity  -u                       TEXT     User or system      │
│                                                          identifier used     │
│                                                          under               │
│                                                          /fsx/analysis_resu… │
│                                                          Defaults to         │
│                                                          --cluster.          │
│    --repository                                 TEXT     Repository key to   │
│                                                          pass to day-clone.  │
│                                                          [default:           │
│                                                          daylily-omics-anal… │
│    --git-tag           -t                       TEXT     Git branch or tag   │
│                                                          passed to           │
│                                                          day-clone.          │
│                                                          [default: main]     │
│    --project                                    TEXT     Project/budget for  │
│                                                          dyoainit.           │
│    --skip-project-ch…      --strict-project…             Skip or enable      │
│                                                          upstream project    │
│                                                          validation in       │
│                                                          dyoainit.           │
│                                                          [default:           │
│                                                          skip-project-check] │
│    --genome                                     TEXT     Genome build.       │
│                                                          [default: hg38]     │
│    --jobs                                       INTEGER  Snakemake job       │
│                                                          count.              │
│                                                          [default: 6]        │
│    --aligners                                   TEXT     Comma-separated     │
│                                                          aligner list.       │
│                                                          [default: bwa2a]    │
│    --dedupers                                   TEXT     Comma-separated     │
│                                                          deduper list.       │
│                                                          [default: dmd]      │
│    --snv-callers                                TEXT     Comma-separated SNV │
│                                                          caller list.        │
│                                                          [default: deep]     │
│    --sv-callers                                 TEXT     Comma-separated SV  │
│                                                          caller list.        │
│    --target                                     TEXT     Workflow target.    │
│                                                          [default:           │
│                                                          produce_snv_concor… │
│    --dy-command                                 TEXT     Override the dy-r   │
│                                                          command entirely.   │
│    --snakemake-extra                            TEXT     Additional          │
│                                                          arguments appended  │
│                                                          to dy-r.            │
│    --no-containerized                                    Disable             │
│                                                          DAY_CONTAINERIZED.  │
│    --export-destinat…                           TEXT     Full S3 prefix      │
│                                                          ending in           │
│                                                          <executing-entity>… │
│                                                          for auto-export.    │
│    --export-trigger                             TEXT     Auto-export         │
│                                                          trigger: none,      │
│                                                          on-success,         │
│                                                          on-fail, or all.    │
│                                                          [default: none]     │
│    --delete-on-expor…                                    Delete the FSx      │
│                                                          analysis directory  │
│                                                          after a successful  │
│                                                          requested export.   │
│    --replace-existin…                                    Explicit retry      │
│                                                          mode: remove an     │
│                                                          existing same       │
│                                                          analysis directory  │
│                                                          before launch.      │
│                                                          Existing analysis   │
│                                                          directories fail    │
│                                                          hard unless this    │
│                                                          flag is set.        │
│    --artifact-regist…                           TEXT     Catalog command id  │
│                                                          whose               │
│                                                          artifact_registrat… │
│                                                          policy should run   │
│                                                          after export.       │
│    --dewey-url                                  TEXT     Dewey base URL for  │
│                                                          post-export         │
│                                                          artifact            │
│                                                          registration.       │
│    --dewey-token-env                            TEXT     Environment         │
│                                                          variable containing │
│                                                          the Dewey bearer    │
│                                                          token.              │
│    --dewey-analysis-…                           TEXT     External object id  │
│                                                          for the exported    │
│                                                          daylily-omics-anal… │
│                                                          S3 directory.       │
│    --dewey-run-artif…                           TEXT     Dewey run artifact  │
│                                                          EUID to link to the │
│                                                          exported analysis   │
│                                                          directory external  │
│                                                          object.             │
│    --dewey-ursa-anal…                           TEXT     Ursa analysis EUID  │
│                                                          to link to the      │
│                                                          exported analysis   │
│                                                          directory external  │
│                                                          object.             │
│    --dry-run                                             Launch a dry-run    │
│                                                          workflow command.   │
│    --help                                                Show this message   │
│                                                          and exit.           │
╰──────────────────────────────────────────────────────────────────────────────╯

