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:false ]

`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:false ]

`${prefix}.bam`
`:file`

consensus BAM file

${prefix}.bam

`versions_fgbio`

`${task.process}`
`:string`

The process the versions were collected from

`fgbio`
`:string`

The tool name

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

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`fgbio`
`:string`

The tool name

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

The expression to obtain the version of the tool

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_fgbio`

`${task.process}`
`:string`

`fgbio`
`:string`

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

Topics

`versions`

`${task.process}`
`:string`

`fgbio`
`:string`

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

Tools

fgbio
MIT

included in

maintainer

get in touch

modules/fgbio_callduplexconsensusreads

Description

Input

meta :map

grouped_bam :file

min_reads :string

min_baseq :integer

Output

bam

meta :map

${prefix}.bam :file

versions_fgbio

${task.process} :string

fgbio :string

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

Topics

versions

${task.process} :string

fgbio :string

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

Tools

fgbioMIT

included in

maintainer

get in touch

`meta`
`:map`

`grouped_bam`
`:file`

`min_reads`
`:string`

`min_baseq`
`:integer`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`versions_fgbio`

`${task.process}`
`:string`

`fgbio`
`:string`

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

`versions`

`${task.process}`
`:string`

`fgbio`
`:string`

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

fgbio
MIT