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

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

Index FASTA file, and optionally generate a file of chromosome sizes

index fasta faidx chromosome

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @drpatelh @ewels @phue

Maintainers: @maxulysse @phue @matthdsm

Index FASTA file, and optionally generate a file of chromosome sizes

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

include { SAMTOOLS_FAIDX } from 'nf-core/samtools/faidx'

MIT License

Process

`Name`	`SAMTOOLS_FAIDX`

Input 2 channels

#1 tuple

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

`get_sizes` boolean	use cut to get the sizes of the index (true) or not (false)

Output 5 channels

#1 fa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{fa,fasta}` file	FASTA file `*.{fa}`

#2 fai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fai` file	FASTA index file `*.{fai}`

#3 gzi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.gzi` file	Optional gzip index file for compressed inputs `*.gzi`

#4 sizes tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sizes` file	File containing chromosome lengths `*.{sizes}`

#5 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` eval	The command used to generate the version of the tool

Tool	Description	Homepage
samtools	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.	http://www.htslib.org/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:10:02 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Ffaidx/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/faidx/blobs/sha256:575b2c681b6e55a6f5a1dfa421f22d66389ec06421da30b8d6b3839e3a9a35d8
Size	3.3 KB
Checksum	sha256:575b2c681b6e55a6f5a1dfa421f22d66389ec06421da30b8d6b3839e3a9a35d8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:10:02 (UTC)		1	3.3 KB	-