Nextflow Registry | nf-core/fcsgx/rungx@0.0.0-6c4ed3a

nf-core/fcsgx/rungx @ 0.0.0-6c4ed3a

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

genome assembly contamination screening cleaning fcs-gx

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @tillenglert @mahesh-panchal

Maintainers: @tillenglert @mahesh-panchal

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

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

include { FCSGX_RUNGX } from 'nf-core/fcsgx/rungx'

MIT License

Process

`Name`	`FCSGX_RUNGX`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`taxid` string	Taxonomy ID of the expected organism
`fasta` file	Input genome assembly file in FASTA format `*.{fa,fasta,fna}`

`gxdb` directory	Directory containing the FCS-GX database

`ramdisk_path` string	Path to RAM disk for improved performance (optional)

Output 5 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.summary.txt` file	FCSGX log file `*.summary.txt`

#2 hits tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.hits.tsv.gz` file	Save intermediate alignments `*.hits.tsv.gz`

#3 fcsgx_report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.fcs_gx_report.txt` file	Final contamination report with contaminant cleaning actions. Interpreted by gx clean genome to separate cleaned sequences from contaminants.

#4 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

#5 taxonomy_report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.taxonomy.rpt` file	Intermediate report with assigned taxonomies to individual sequences. `*.taxonomy.rpt`

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

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:17:08 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ffcsgx%2Frungx/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/fcsgx/rungx/blobs/sha256:646197c257147a166229ff60eb4354eadd7c9aef8deebbadac6ded5ed20a9ad7
Size	3.7 KB
Checksum	sha256:646197c257147a166229ff60eb4354eadd7c9aef8deebbadac6ded5ed20a9ad7
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:17:08 (UTC)		4	3.7 KB