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circrna live audit (2026-08-23)

Original workflow (not an upstream port) · Repo: oxo-flow-circrna (Traitome org, entry file circrna.oxoflow) · Rating: live-verified (data/pipelines.json).

Four independent circRNA callers (CIRIquant, CIRCexplorer2, find_circ, circRNA_finder) + fastp QC + ensemble aggregation (≥2 callers agree). Reference indexes (bowtie2/STAR/bwa/hisat2) and conda envs build automatically on first run; samples auto-discovered from raw/.

Live re-verification (2026-08-23)

Engine: latest main (post-v0.14.1) · Box: tx-ubuntu · Mode: real CLI run, not dry-run · -j 2 --keep-going · exit 0, one round, zero fixes.

  • 4 reference indexes auto-built (1.2kb synthetic genome, seconds)
  • 9 rules all passed: fastp → 4 callers → multiqc → aggregate → aggregate_dataset → report; 12 output files verified
  • Real signal: find_circ detected the planted BSJ chr1:520-719 + 20 reads circ_000001 — exactly matching the fixture's designed e3→e2 back-splice position
  • CIRIquant ran for real: 19 candidate splice-signal reads → second-scan PEM 0 → 0 circRNA (below the statistical threshold of the tiny fixture)
  • circRNA_finder produced real STAR Chimeric.out.junction / SJ.out.tab outputs; no candidates passed its filters

Honest coverage note

All 4 callers executed for real. 1/4 detected the planted BSJ; 3/4 reported 0 circRNAs because the mini fixture (200 read pairs, 1kb genome) sits below their detection thresholds — a statistical limit of the fixture, not a tool or port defect. The report rule's guard echo (WARNING not created) is rule-internal logic; exit 0 is correct.

Usability note

Entry file is circrna.oxoflow, not the main.oxoflow convention — auto-discovery still finds it (alphabetically first *.oxoflow), but renaming to main.oxoflow would align with the other community repos. Pending owner decision.