                                                                                
 Usage: dyec samples stage [OPTIONS] ANALYSIS_SAMPLES                           
                                                                                
 Stage analysis samples and generate workflow manifests.                        
                                                                                
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ *    analysis_samples      PATH  Path to analysis_samples.tsv. [required]    │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ *  --reference-s3-uri                 TEXT     S3 URI mapped to              │
│                                                /fsx/references.              │
│                                                [required]                    │
│ *  --control-data-s3-uri              TEXT     S3 URI mapped to              │
│                                                /fsx/control_data.            │
│                                                [required]                    │
│ *  --stage-s3-uri                     TEXT     S3 URI used as the exact root │
│                                                for external staging          │
│                                                remote_stage_* prefixes.      │
│                                                [required]                    │
│    --config-dir                       PATH     Directory for generated       │
│                                                samples.tsv and units.tsv.    │
│    --stage-target                     TEXT     FSx staging base directory.   │
│                                                [default:                     │
│                                                /fsx/staging/staged_external… │
│    --run-metric-staging               TEXT     Copy run metric files into    │
│                                                runs/<RUN_UID>/ from          │
│                                                RUN_UID:PLATFORM:FOFN. Can be │
│                                                specified multiple times.     │
│    --profile                          TEXT     AWS CLI profile. Defaults to  │
│                                                AWS_PROFILE env var.          │
│    --region                           TEXT     AWS region. Defaults to       │
│                                                AWS_REGION/AWS_DEFAULT_REGIO… │
│    --cluster,--cluster-name           TEXT     ParallelCluster name for      │
│                                                creating the staged-prefix    │
│                                                FSx DRA.                      │
│    --fsx-file-system-id               TEXT     FSx file system id for        │
│                                                creating the staged-prefix    │
│                                                DRA.                          │
│    --staging-mount-timeout-se…        INTEGER  Seconds to wait for the       │
│                                                staged-prefix DRA to become   │
│                                                available.                    │
│                                                [default: 900]                │
│    --debug                                     Print AWS CLI commands before │
│                                                execution.                    │
│    --precheck-only                             Validate the manifest and     │
│                                                exit without staging or       │
│                                                writing generated configs.    │
│    --config-only                               Validate the manifest and     │
│                                                write generated               │
│                                                samples.tsv/units.tsv locally │
│                                                without creating a            │
│                                                staged-prefix DRA.            │
│    --help                                      Show this message and exit.   │
╰──────────────────────────────────────────────────────────────────────────────╯

