Nextflow Registry | nf-core/ngsbits/samplegender@0.0.0-0c7146d

nf-core/ngsbits/samplegender @ 0.0.0-0c7146d

Determines the gender of a sample from the BAM/CRAM file.

gender cram bam short reads

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Determines the gender of a sample from the BAM/CRAM file.

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

include { NGSBITS_SAMPLEGENDER } from 'nf-core/ngsbits/samplegender'

MIT License

Process

`Name`	`NGSBITS_SAMPLEGENDER`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	One or more BAM/CRAM files to determine the gender of `*.{bam,cram}`
`bai` file	The index file(s) from the input BAM/CRAM file(s) `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference fasta information e.g. [ id:'test' ]
`fasta` file	The reference FASTA to use (mandatory when CRAM files are used) `*.{fasta,fa,fna}`

#3 tuple

`meta3` map	Groovy Map containing reference fasta information e.g. [ id:'test' ]
`fai` file	The index file from the reference FASTA `*.fai`

`method` string	The method to use to define the gender (possibilities are 'xy', 'hetx' and 'sry') `(xy\|hetx\|sry)`

Output 2 channels

#1 tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tsv` file	An output TSV file containing the results of the gender prediction `*.tsv`

#2 versions_ngsbits tuple

`${task.process}` string	The name of the process
`ngsbits` string	The name of the tool
`SampleGender --version 2>&1 \| sed 's/SampleGender //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
ngsbits	Short-read sequencing tools	https://github.com/imgag/ngs-bits

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:58:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fngsbits%2Fsamplegender/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ngsbits/samplegender/blobs/sha256:fbca42670b362a74ffa5e919438a3df7cc63991dee7aedc987140011b99d79f2
Size	2.5 KB
Checksum	sha256:fbca42670b362a74ffa5e919438a3df7cc63991dee7aedc987140011b99d79f2
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:58:55 (UTC)		1	2.5 KB	-