Description

Converts a SAM/BAM/CRAM file to FASTQ

Input

name:type
description
pattern

meta:map

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

]

input:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

interleave:boolean

Set true for interleaved fastq file

Output

name:type
description
pattern

fastq

meta:map

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

]

*_{1,2}.fastq.gz:file

Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.

*_{1,2}.fastq.gz

interleaved

meta:map

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

]

*_interleaved.fastq:file

Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.

*_interleaved.fastq.gz

singleton

meta:map

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

]

*_singleton.fastq.gz:file

Compressed FASTQ file with singleton reads

*_singleton.fastq.gz

other

meta:map

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

]

*_other.fastq.gz:file

Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset

*_other.fastq.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.