OmniBioAI

circTools Runner

Run circtools detect on STAR staged outputs from workflow_runner.

Goal Graph FASTQ → circRNA samplesheet.csv

Run circTools detect on the staged STAR tree produced by workflow_runner. Expected STAR tree layout: samplesheet.csv, mate1/, mate2/, bam_files.txt.

STAR tree directory (path)

Optional if you provide STAR tree OmniObject ID instead.

STAR tree OmniObject ID

Preferred in production. Resolves to a local path.

gencode nodot GTF (OmniObject)

repeat GTF (OmniObject)

genome FASTA (OmniObject)

Nr range

Maps to: -Nr <min> <max>

Flags

-Pi -F -M -fg -G

Expected STAR tree layout: samplesheet.csv, mate1/, mate2/, bam_files.txt.