- id: salmon-index-source-type
  status: resolved
  kind: gap
  blocking: false
  raised_by: freeform-summary-to-galaxy-interface
  step: salmon_quant
  unmet: "Salmon reference index source format"
  missing: "Whether reference target is supplied as pre-built index archive or FASTA for index creation"
  resolved_by: advance-galaxy-draft-step
  supersedes: null
  note: "Resolved to history-supplied reference transcriptome FASTA with on-the-fly k-mer indexing (k=31)."

- id: deseq2-design-formula-specification
  status: resolved
  kind: gap
  blocking: false
  raised_by: freeform-summary-to-galaxy-interface
  step: deseq2
  unmet: "Multi-factor formula and primary contrast"
  missing: "Exact factor order and whether interaction term Genotype:Condition is modeled"
  resolved_by: advance-galaxy-draft-step
  supersedes: null
  note: "Resolved using sample_sheet_contrasts with custom design formula ~ Genotype + Timepoint + Condition and tximport integration."