Nextflow Registry | nf-core/hostile/clean@0.0.0-0c7146d

nf-core/hostile/clean @ 0.0.0-0c7146d

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

hostile decontamination human removal host removal clean

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:48:15 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhostile%2Fclean/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hostile/clean/blobs/sha256:08282901f68b96090131052c983adc2ebb333df3391ee928f39b524932cd961a
Size	3.5 KB
Checksum	sha256:08282901f68b96090131052c983adc2ebb333df3391ee928f39b524932cd961a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:48:15 (UTC)		1	3.5 KB	-