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

:map

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

reads

:file

pair of reads to be converted into BAM file

*.{fastq.gz}

Output

name:type
description
pattern

bam

meta

:map

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

*.{bam,cram}

:file

Unaligned, unsorted BAM or CRAM file

*.{bam,cram}

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 https://github.com/fulcrumgenomics/fgbio
included in
radseqsarek
maintainers
Github user lescai
Github user matthdsm
Github user nvnieuwk
get in touch
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