Description

Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

pair of reads to be converted into BAM file

*.{fastq.gz}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.{bam,cram}{:bash}

:file

Unaligned, unsorted BAM or CRAM file

*.{bam,cram}

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

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 https://github.com/fulcrumgenomics/fgbio
included in
radseqsarek
maintainers
Github user lescai
Github user matthdsm
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub