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:false ]

`mapped_bam`
`:file`

mapped BAM/SAM file

*.{bam,sam}

`unmapped_bam`
`:file`

unmapped BAM file

*.bam

`meta2`
`:map`

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

`fasta`
`:file`

fasta file containing genomic sequence information

*.{fasta,fna,fa}

`index`
`:file`

fasta index file

*.fai

`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:false ]

`${prefix}.bam`
`:file`

Zipped BAM file

*.bam

`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

modules/fgbio_zipperbams

Description

Input

`meta`
`:map`

`mapped_bam`
`:file`

`unmapped_bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index`
`:file`

`dict`
`:file`

Output

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`versions_fgbio`

`${task.process}`
`:string`

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

Tools

fgbio
MIT

included in

maintainer

get in touch

modules/fgbio_zipperbams

Description

Input

meta:map

mapped_bam:file

unmapped_bam:file

meta2:map

fasta:file

index:file

dict:file

Output

bam

meta:map

${prefix}.bam:file

versions_fgbio

${task.process}:string

fgbio:string

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//":eval

Topics

versions

${task.process}:string

fgbio:string

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//":eval

Tools

fgbio MIT

included in

maintainer

get in touch

`meta`
`:map`

`mapped_bam`
`:file`

`unmapped_bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index`
`:file`

`dict`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`versions_fgbio`

`${task.process}`
`:string`

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

`versions`

`${task.process}`
`:string`

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

fgbio
MIT