modules/fgbio_zipperbams

FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM

fgbioumiunmappedubamzipperbams

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

Description

FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM

Input

name:type

description

pattern

`meta:map`

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

]

`unmapped_bam:file`

unmapped BAM file

*.bam

`meta2:map`

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

]

`mapped_bam:file`

mapped BAM/SAM file

*.{bam,sam}

`meta3:map`

Groovy Map containing reference information e.g. [ id:‘GRCh38’ ]

`fasta:file`

fasta file containing genomic sequence information

*.{fasta,fa}

`meta4:map`

Groovy Map containing reference information e.g. [ id:‘GRCh38’ ]

`dict:file`

dict file containing a sequence dictionary for the fasta file

*.{dict}

Output

name:type

description

pattern

`bam`

`meta:map`

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

]

`${prefix}.bam:file`

Zipped BAM file

*.bam

`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_zipperbams

Description

Input

meta:map

unmapped_bam:file

meta2:map

mapped_bam:file

meta3:map

fasta:file

meta4:map

dict:file

Output

bam

meta:map

${prefix}.bam:file

versions

versions.yml:file

Tools

fgbio MIT

`meta:map`

`unmapped_bam:file`

`meta2:map`

`mapped_bam:file`

`meta3:map`

`fasta:file`

`meta4:map`

`dict:file`

`bam`

`meta:map`

`${prefix}.bam:file`

`versions`

`versions.yml:file`

fgbio
MIT