modules/gatk4_samtofastq

Converts BAM/SAM file to FastQ format

bedgatk4interval_list

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

Description

Converts BAM/SAM file to FastQ format

Input

name:type

description

pattern

`meta:map`

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

`bam:file`

Input SAM/BAM file

*.{bam,sam}

Output

name:type

description

pattern

`fastq`

`meta:file`

converted fastq file

*.fastq

`*.fastq.gz:file`

converted fastq file

*.fastq

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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_samtofastq

Description

Input

meta:map

bam:file

Output

fastq

meta:file

*.fastq.gz:file

versions

versions.yml:file