Nextflow Registry | nf-core/samtools/collatefastq@0.0.0-0c7146d

nf-core/samtools/collatefastq @ 0.0.0-0c7146d

The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format

bam2fq samtools fastq

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @lescai @maxulysse @matthdsm

The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format

Add the following snippet to your workflow script to include this module.

include { SAMTOOLS_COLLATEFASTQ } from 'nf-core/samtools/collatefastq'

MIT License

Process

`Name`	`SAMTOOLS_COLLATEFASTQ`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference genome file `*.{fa,fasta}`
`fai` file	Reference genome index file `*.fai`

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

Output 5 channels

#1 fastq tuple

`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`

#2 fastq_other tuple

`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`

#3 fastq_singleton tuple

`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`

#4 fastq_interleaved tuple

`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`

#5 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
samtools	Tools for dealing with SAM, BAM and CRAM files	http://www.htslib.org

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fcollatefastq/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/collatefastq/blobs/sha256:e19c80c52c18fdcc8b456c2f9c9f951548fc3a9c99675efbcd43721ebc93cadf
Size	3.4 KB
Checksum	sha256:e19c80c52c18fdcc8b456c2f9c9f951548fc3a9c99675efbcd43721ebc93cadf
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:49 (UTC)