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

reads (file)

pair of reads to be converted into BAM file

*.{fastq.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

version (file)

File containing software version

*.{version.yml}

bam (file)

Unaligned, unsorted BAM file

*.{bam}

cram (file)

Unaligned, unsorted CRAM file

*.{cram}
included in
sarek
authors
Github user lescai Github user matthdsm
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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