Nextflow Registry | nf-core/htslib/bgziptabix@0.0.0-9ed7f15

nf-core/htslib/bgziptabix @ 0.0.0-9ed7f15

Multi-purpose module to compress, decompress and index files using bgzip and tabix.

compress decompress index bgzip tabix gzip bzip xz

Latest version: 0.0.0-9ed7f15

Total downloads: 0

Source: nf-core/modules

Authors: @itrujnara

Maintainers: @itrujnara

Multi-purpose module to compress, decompress and index files using bgzip and tabix.

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

include { HTSLIB_BGZIPTABIX } from 'nf-core/htslib/bgziptabix'

MIT License

Process

`Name`	`HTSLIB_BGZIPTABIX`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`infile` file	Input file to compress or decompress `*`
`infile_tbi` file	Optional tabix index for the input file. `*.{tbi,csi}`
`regions` file	Optional file of regions to extract (BED or chr:start-end format). Only used when creating an index for the output file. `*.{bed,txt,tsv}`

`action` string	Action to perform, either `compress` or `decompress`

`make_index` boolean	Whether to create a tabix index for the output file; only used if `action` is `compress`

`out_ext` string	Output file extension without `.gz` suffix (for example `vcf`)

Output 4 channels

#1 index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${outfile}.{tbi,csi}` file	Tabix index file for the compressed output file `*.{tbi,csi}`

#2 output tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${outfile}` file	Compressed or decompressed output file `*`

#3 versions_xz tuple

`${task.process}` string	The name of the process
`xz` string	The name of the tool
`xz --version \| sed '1! d; s/xz (XZ Utils) //'` eval	The expression to obtain the version of the tool

#4 versions_htslib tuple

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

Tool	Description	Homepage
htslib	C library for high-throughput sequencing data formats.	http://www.htslib.org/

Version	0.0.0-9ed7f15
Commit ID	9ed7f157dd96f83b852da7ea4d3a217907f50f36
Release Date	22 May 2026 15:00:55 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fhtslib%2Fbgziptabix/0.0.0-9ed7f15/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/htslib/bgziptabix/blobs/sha256:162593f083139ef5d14e7e187d5649893c1bf6137ba2b3dc429c4e7408d5fc2a
Size	4.6 KB
Checksum	sha256:162593f083139ef5d14e7e187d5649893c1bf6137ba2b3dc429c4e7408d5fc2a
Downloads	0

Version	Date	Status	Downloads	Size	Diff
0.0.0-9ed7f15	22 May 2026 15:00:55 (UTC)