modules/gatk4_addorreplacereadgroups

Assigns all the reads in a file to a single new read-group

addreplaceread-grouppicardgatk

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/addorreplacereadgroups

Description

Assigns all the reads in a file to a single new read-group

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Input BAM file

*.{bam}

`meta2`
`:map`

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

`fasta`
`:file`

Reference genome file

*.{fasta,fa,fasta.gz,fa.gz}

`meta3`
`:map`

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

`fasta_index`
`:file`

Reference genome index file

*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Output BAM file

*.{bam}

`bai`

`meta`
`:map`

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

`*.bai`
`:file`

An optional BAM index file

*.{bai}

`cram`

`meta`
`:map`

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

`*.cram`
`:file`

Output CRAM file

*.{cram}

`versions_gatk4`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590

modules/gatk4_addorreplacereadgroups

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_index`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
Apache-2.0

included in

maintainers

get in touch

modules/gatk4_addorreplacereadgroups

Description

Input

meta:map

bam:file

meta2:map

fasta:file

meta3:map

fasta_index:file

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

cram

meta:map

*.cram:file

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_index`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
Apache-2.0