Description

Converts FastQ file to SAM/BAM format

Input

name:type
description
pattern

meta

:map

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

reads

:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

*.fastq.gz

Output

name:type
description
pattern

bam

meta

:map

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

*.bam

:file

Converted BAM file

*.bam

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
MIT

Genome Analysis Toolkit (GATK4) 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 https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
maintainer
Github user ntoda03
get in touch
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