Description

The module uses collate and then fastq methods 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

]

input (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

meta2 (map)

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

fasta (file)

Reference genome fasta file

*.{fasta,fa}

interleave (boolean)

If true, the output is a single interleaved paired-end FASTQ
If false, the output split paired-end FASTQ

Output

Name (Type)
Description
Pattern

meta (map)

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

]

fastq (file)

R1 and R2 FASTQ files

*_{1,2}.fq.gz

fastq_interleaved (file)

Interleaved paired end FASTQ files

*_interleaved.fq.gz

fastq_other (file)

FASTQ files with reads where the READ1 and READ2 FLAG bits set are either both set or both unset.

*_other.fq.gz

fastq_singleton (file)

FASTQ files with singleton reads.

*_singleton.fq.gz

versions (file)

File containing software versions

versions.yml
included in
bamtofastq hlatyping rnadnavar sarek
maintainers
Github user lescai
Github user maxulysse
Github user matthdsm
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

samtools
MIT

Tools for dealing with SAM, BAM and CRAM files

http://www.htslib.org/doc/1.1/samtools