modules/gatk4_printreads

Print reads in the SAM/BAM/CRAM file

bamcramgatk4printreadssam

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

Description

Print reads in the SAM/BAM/CRAM file

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`index`
`:file`

BAM/CRAM/SAM file

*.{bai,crai,sai}

`meta2`
`:map`

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

`fasta`
`:file`

reference fasta file

*.{fa,fasta}

`meta3`
`:map`

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

`fai`
`:file`

reference fasta index file

*.{fai}

`meta4`
`:map`

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

`dict`
`:file`

reference fasta dictionary 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`

Sorted BAM file

*.{bam}

`cram`

`meta`
`:map`

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

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

Sorted CRAM file

*.{cram}

`sam`

`meta`
`:map`

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

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

Sorted SAM file

*.{sam}

`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_printreads

Description

Input

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

Output

`bam`

`meta`
`:map`

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

`cram`

`meta`
`:map`

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

`sam`

`meta`
`:map`

`${prefix}.sam`
`: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_printreads

Description

Input

meta:map

input:file

index:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

Output

bam

meta:map

${prefix}.bam:file

cram

meta:map

${prefix}.cram:file

sam

meta:map

${prefix}.sam: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`

`input`
`:file`

`index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`bam`

`meta`
`:map`

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

`cram`

`meta`
`:map`

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

`sam`

`meta`
`:map`

`${prefix}.sam`
`: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