Nextflow Registry | nf-core/fcsgx/cleangenome@0.0.0-3fc6d40

nf-core/fcsgx/cleangenome @ 0.0.0-3fc6d40

Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies

genome assembly contamination screening cleaning fcs-gx

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @mahesh-panchal @LaurenHuet

Maintainers: @mahesh-panchal

Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies

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

include { FCSGX_CLEANGENOME } from 'nf-core/fcsgx/cleangenome'

MIT License

Process

`Name`	`FCSGX_CLEANGENOME`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	Input genome assembly file in FASTA format `*.{fa,fasta,fna}`
`fcsgx_report` file	Final contamination report with contaminant cleaning actions. Generated using FCSGX_RUNGX

Output 3 channels

#1 cleaned tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.cleaned.fasta` file	The fasta file after cleaning, where sequences annotated as ACTION_EXCLUDE or ACTION_TRIM are excluded

#2 contaminants tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.contaminants.fasta` file	Sequences annotated as ACTION_EXCLUDE which are marked as contaminants.

#3 versions_fcsgx tuple

`${task.process}` string	The name of the process
`fcsgx` string	The name of the tool
`gx --help \| sed '/build/!d; s/.:v//; s/-.//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
fcsgx	The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.	https://github.com/ncbi/fcs-gx

Version	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:12:05 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ffcsgx%2Fcleangenome/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/fcsgx/cleangenome/blobs/sha256:894c2e76da0f9fe7ae68e2c4e1e8c594768d03dc528272228e445cba046e5142
Size	2.7 KB
Checksum	sha256:894c2e76da0f9fe7ae68e2c4e1e8c594768d03dc528272228e445cba046e5142
Downloads	2

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:17:05 (UTC)	3	2.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:12:05 (UTC)	2	2.7 KB
0.0.0-0c7146d	08 Apr 2026 19:00:44 (UTC)	3	2.7 KB