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{:bash}

:map

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

grouped_bam{:bash}

:file

Grouped BAM file

*.bam

min_reads{:bash}

: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{:bash}

:integer

Ignore bases in raw reads that have Q below this value

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

${prefix}.bam{:bash}

:file

consensus BAM file

${prefix}.bam

versions_fgbio{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fgbio{:bash}

:string

The tool name

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fgbio{:bash}

:string

The tool name

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
radseq
maintainer
Github user lescai
get in touch
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