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:false ]

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

fastq

meta:map

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

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

R1 and R2 FASTQ files

*_{1,2}.fq.gz

fastq_interleaved

meta:map

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

*_interleaved.fq:file

Interleaved paired end FASTQ files

*_interleaved.fq.gz

fastq_other

meta:map

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

*_other.fq.gz: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

meta:map

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

*_singleton.fq.gz:file

FASTQ files with singleton reads.

*_singleton.fq.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bamtofastq hlatyping rnadnavar sarek
Github user lescai
Github user maxulysse
Github user matthdsm
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