Nextflow Registry | nf-core/hostile/clean@0.0.0-6c4ed3a

nf-core/hostile/clean @ 0.0.0-6c4ed3a

Removes host reads from short- and long-read FASTQ sequencing files

hostile decontamination human removal host removal clean

Latest version: 0.0.0-6c4ed3a

Total downloads: 12

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

Removes host reads from short- and long-read FASTQ sequencing files

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

include { HOSTILE_CLEAN } from 'nf-core/hostile/clean'

MIT License

Process

`Name`	`HOSTILE_CLEAN`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`reads` file	Paired or single end FASTQ files `*.{fastq,fq,fastq.gz,fq.gz}`

#2 tuple

`reference_name` string	Name of the reference to align against and thus remove mapped reads to.
`reference_dir` directory	Directory containing index file(s) corresponding to the preferred aligner (bowtie2 short reads or minimap for long reads). Note that single end data is assumed to be long reads. If you have single-end short read you must supply both the BowTie2 indices AND explicitly specify `--aligner bowtie2`

Output 3 channels

#1 json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.json` file	JSON report containing statistics from hostile cleaning `*.json`

#2 fastq tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.fastq.gz` file	Cleaned FASTQ files with host reads removed `*.{fastq,fq,fastq.gz,fq.gz}`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
hostile	Hostile: accurate host decontamination	https://github.com/bede/hostile

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:24:37 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fhostile%2Fclean/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/hostile/clean/blobs/sha256:902dd625ff01424776f2e47e7d5afcffd885de7ba8ef122e95ba5e18c75518ec
Size	3.5 KB
Checksum	sha256:902dd625ff01424776f2e47e7d5afcffd885de7ba8ef122e95ba5e18c75518ec
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:24:37 (UTC)	3	3.5 KB
0.0.0-7f68141	16 Apr 2026 15:01:03 (UTC)	3	3.5 KB
0.0.0-02a6b4c	13 Apr 2026 15:00:33 (UTC)	3	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:10:03 (UTC)	3	3.5 KB