modules/gatk4_splitncigarreads

Splits reads that contain Ns in their cigar string

gatk4mergevcf

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

Description

Splits reads that contain Ns in their cigar string

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:list`

BAM/SAM/CRAM file containing reads

*.{bam,sam,cram}

`bai`
`:list`

BAI/SAI/CRAI index file (optional)

*.{bai,sai,crai}

`intervals`
`:file`

Bed file with the genomic regions included in the library (optional)

`meta2`
`:map`

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

`fasta`
`:file`

The reference fasta file

*.fasta

`meta3`
`:map`

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

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`meta4`
`:map`

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

`dict`
`:file`

GATK sequence dictionary

*.dict

Output

name:type

description

pattern

`bam`

`meta`
`:file`

Output file with split reads (BAM/SAM/CRAM)

*.{bam,sam,cram}

`*.bam`
`:file`

Output file with split reads (BAM/SAM/CRAM)

*.{bam,sam,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_splitncigarreads

Description

Input

`meta`
`:map`

`bam`
`:list`

`bai`
`:list`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

Output

`bam`

`meta`
`:file`

`*.bam`
`: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

maintainer

get in touch

modules/gatk4_splitncigarreads

Description

Input

meta:map

bam:list

bai:list

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

Output

bam

meta:file

*.bam: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

maintainer

get in touch

`meta`
`:map`

`bam`
`:list`

`bai`
`:list`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`bam`

`meta`
`:file`

`*.bam`
`: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