modules/fgbio_fastqtobam

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

unalignedbamcram

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

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:file`

Unaligned, unsorted BAM file

*.{bam}

`cram`

`meta:map`

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

`*.cram:file`

Unaligned, unsorted CRAM file

*.{cram}

`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 https://github.com/fulcrumgenomics/fgbio

modules/fgbio_fastqtobam

Description

Input

meta:map

reads:file

Output

bam

meta:map

*.bam:file

cram

meta:map

*.cram:file

versions

versions.yml:file

Tools

fgbio MIT

`meta:map`

`reads:file`

`bam`

`meta:map`

`*.bam:file`

`cram`

`meta:map`

`*.cram:file`

`versions`

`versions.yml:file`

fgbio
MIT