helixforge doctor

Preflight: validate inputs + resolve external tools before a run.

The single input-validation entry point, run it before a real reconcile. With no inputs it resolves and versions every external tool the pipeline shells out to (mikado, diamond, transdecoder, portcullis, …) and checks environment hygiene (console-script shim, CRAM reference). Given --genome + --helixer (and optional evidence) it also runs the input-integrity preflight: seqid concordance across inputs, GFF3/GTF/FASTA/BAM format sniffing, and BAM/CRAM index (CSI) presence. --check-config verifies an emitted Mikado config/scoring file against the detected Mikado version.

Nothing is modified and nothing is annotated, this command only inspects. It exits non-zero if a required tool is missing, an emitted config fails schema verification, or the input-integrity gate fails.

Reports (printed to the console; advisory checks warn, gates fail):

• external-tool table: tool, resolved path, detected version, status
• environment hygiene: console-script shim, CRAM-reference readiness
• (optional) Mikado config/scoring verification verdict
• (optional) input-integrity report: seqid concordance, format, index

Options

Option	Description
--mikado-bin	Override the mikado binary.
--diamond-bin	Override the diamond binary.
--check-config	Verify an emitted Mikado configuration.yaml against the detected version.
--check-scoring	Scoring YAML to verify alongside --check-config.
--genome	Genome FASTA (integrity check).
--helixer	Helixer GFF3 (integrity check).
--helixer-h5	Helixer HDF5 (integrity check).
--stringtie	StringTie GTF (repeatable). (repeatable)
--bam	RNA-seq BAM (repeatable). (repeatable)
--star-sj	STAR SJ.out.tab (repeatable). (repeatable)
--miniprot	miniprot GFF (integrity check).
--reference	Genome FASTA for CRAM decode, doctor reports whether CRAM BAM inputs have an offline reference (--reference or REF_CACHE).
--seqid-aliases	Seqid alias map (JSON {alias: canonical} or 2-col TSV).

Examples

  # just the external-tool preflight (mikado, diamond, …)
  helixforge doctor

  # tools + input-integrity (seqid concordance / format sniff / BAM index)
  helixforge doctor --genome genome.fa --helixer helixer.gff3 \
      --helixer-h5 helixer.h5 --bam sampleA.bam --star-sj sampleA.SJ.out.tab

  # verify an emitted Mikado config/scoring against the detected mikado version
  helixforge doctor --check-config configuration.yaml --check-scoring scoring.yaml