robin utils¶
Utility subcommands for assets, reference/panel staging, and post-hoc MGMT summaries. The group is separate from the live workflow so you can update models or prepare files without starting the orchestrator.
Subcommands documented below:
| Command | Purpose |
|---|---|
update-models | Download or refresh model files from the assets manifest. |
update-clinvar | Update ClinVar resources used for annotation paths. |
sequencing-files | Copy panel BED(s) and download or link a GRCh38 FASTA for MinKNOW / alignment. |
mgmt | Tabulate MGMT CpG methylation from existing mgmt_sorted.bam outputs. |
robin utils update-models¶
Downloads or refreshes model files (checksums via the manifest). Typical after install or when assets change.
| Option | Description |
|---|---|
--models-dir | Override output directory (default: ROBIN models directory). |
--manifest | Path to assets.json (default: packaged manifest or ROBIN_ASSETS_MANIFEST). |
--overwrite | Replace existing files. |
For private GitHub-hosted assets, set GITHUB_TOKEN before running.
More context: Installation — models.
robin utils update-clinvar¶
Updates ClinVar in ROBIN’s resource tree (best-effort “newer NCBI drop” behaviour).
Pair with update-models when setting up a new environment.
robin utils sequencing-files¶
Stages panel BED files and a reference FASTA into one folder for MinKNOW (adaptive sampling + alignment) and for passing the same path to robin workflow --reference.
| Option | Description |
|---|---|
-p / --panel | Required. Panel name (same as --target-panel). |
-r / --reference | URL to download or local .fa / .fa.gz. Default: NCBI GRCh38 no-alt (large download). |
-o / --output-dir | Output directory (default: ./reference_files). |
-y / --yes | Non-interactive confirmation. |
The command copies packaged {panel}_panel_name_uniq.bed and, when present, {panel}_panel_source.bed, then materializes the reference.
See also: Quickstart — Reference and panel BEDs.
robin utils mgmt¶
Summarises MGMT CpG methylation from mgmt_sorted.bam files already produced under a ROBIN output tree (offline inspection / QC).
| Option | Description |
|---|---|
OUTPUT_DIR | Root directory to search (required). |
-r / --recursive | Find mgmt_sorted.bam recursively. |
-o / --out | TSV path; default - (stdout). |