`robin list-job-types` and job model¶

robin list-job-types prints the job types ROBIN knows about, grouped by queue. Understanding this helps you build -w / --workflow strings for robin workflow.

Command¶

robin list-job-types

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Queues and job types¶

The orchestration layer assigns each job type to a queue (simplified names here; internal Ray queue names may differ slightly):

Queue (concept)	Job types	Role
Preprocessing	`preprocessing`	Read BAM headers/metadata; entry point for each new file.
BED conversion	`bed_conversion`	Prepare inputs for classifiers that need BED-level views.
Analysis	`mgmt`, `cnv`, `target`, `fusion`	Methylation (MGMT), copy number, targeted variant/fusion panels.
Classification	`sturgeon`, `nanodx`, `pannanodx`	Methylation / expression classifiers.
Slow	`random_forest`	Heavier or batched models.

Automatic steps¶

When you use the simplified workflow format (-w mgmt,sturgeon, …):

preprocessing is prepended if you did not list it.
bed_conversion is inserted when any of sturgeon, nanodx, pannanodx, or random_forest appear — those jobs expect BED conversion upstream.

You do not need to list bed_conversion manually for those classifiers unless you are hand-editing legacy queue-prefixed pipelines.

Valid job type names¶

The CLI accepts only these job identifiers in workflow strings:

preprocessing, bed_conversion, mgmt, cnv, target, fusion, sturgeon, nanodx, pannanodx, random_forest

Unknown names produce warnings and are skipped.

Examples¶

# Minimal classifier run (preprocessing + bed_conversion added as needed)
robin workflow /data/bams -w sturgeon --center Demo --target-panel rCNS2 -d /out --reference /ref/hg38.fa

# Full stack (typical)
robin workflow /data/bams \
  -w target,cnv,fusion,mgmt,sturgeon,nanodx,pannanodx,random_forest \
  --center Sherwood \
  --target-panel rCNS2 \
  -d ~/results \
  --reference ~/references/hg38.fa

robin list-job-types and job model¶