Description

Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM/SAM file, grouped by UMI

*.{bam,sam}

min_reads (string)

Minimum number of raw/original reads to build each consensus read. Can be a space delimited list of 1-3 values. See fgbio documentation for more details.

min_baseq (integer)

Ignore bases in raw reads that have Q below this value

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

bam (file)

consensus BAM file

*.bam