Description

The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format

Input

name:type
description
pattern

meta:map

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

]

inputbam:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

split:boolean

TRUE/FALSE value to indicate if reads should be separated into /1, /2 and if present other, or singleton. Note: choosing TRUE will generate 4 different files. Choosing FALSE will produce a single file, which will be interleaved in case the input contains paired reads.

Output

name:type
description
pattern

reads

meta:map

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

]

*.fq.gz:file

FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) or a single interleaved .fq.gz file if the user chooses not to split the reads.

*.fq.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

samtools
MIT

Tools for dealing with SAM, BAM and CRAM files

http://www.htslib.org/doc/1.1/samtools
included in
rnadnavar sarek
maintainer
Github user lescai
get in touch
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