modules/fgbio_callduplexconsensusreads

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

umiduplexfgbio

https://github.com/nf-core/modules/[...]/modules/nf-core/fgbio/callduplexconsensusreads

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

]

`grouped_bam:file`

Grouped BAM file

*.bam

`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

`bam`

`meta:map`

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

]

`${prefix}.bam:file`

consensus BAM file

*.bam

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

fgbio
MIT

A set of tools for working with genomic and high throughput sequencing data, including UMIs

http://fulcrumgenomics.github.io/fgbio http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads https://github.com/fulcrumgenomics/fgbio

modules/fgbio_callduplexconsensusreads

Description

Input

meta:map

grouped_bam:file

min_reads:string

min_baseq:integer

Output

bam

meta:map

${prefix}.bam:file

versions

versions.yml:file

Tools

fgbio MIT

`meta:map`

`grouped_bam:file`

`min_reads:string`

`min_baseq:integer`

`bam`

`meta:map`

`${prefix}.bam:file`

`versions`

`versions.yml:file`

fgbio
MIT