Nextflow Registry | nf-core/fcs/fcsadaptor@0.0.0-0c7146d

nf-core/fcs/fcsadaptor @ 0.0.0-0c7146d

Run NCBI's FCS adaptor on assembled genomes

assembly genomics quality control contamination NCBI

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @d4straub

Maintainers: @d4straub @gallvp

Run NCBI's FCS adaptor on assembled genomes

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

include { FCS_FCSADAPTOR } from 'nf-core/fcs/fcsadaptor'

MIT License

Process

`Name`	`FCS_FCSADAPTOR`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`assembly` file	assembly fasta file

Output 6 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fcs_adaptor.log` file	Log file `*.{fcs_adaptor.log}`

#2 pipeline_args tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pipeline_args.yaml` file	Run arguments `*.{pipeline_args.yaml}`

#3 skipped_trims tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.skipped_trims.jsonl` file	Skipped trim information `*.{skipped_trims.jsonl}`

#4 adaptor_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fcs_adaptor_report.txt` file	Report of identified adaptors `*.{fcs_adaptor_report.txt}`

#5 cleaned_assembly tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cleaned_sequences.fa.gz` file	Cleaned assembly in fasta format `*.{cleaned_sequences.fa.gz}`

#6 versions_fcsadaptor tuple

`${task.process}` string	The name of the process
`fcsadaptor` string	The name of the tool
`0.5.0` string	The expression to obtain the version of the tool

Tool	Description	Homepage
fcs	The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly.	https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:38:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ffcs%2Ffcsadaptor/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/fcs/fcsadaptor/blobs/sha256:7e5f8ab472f973a38025ba261aa6a997e8851c79d33299f260f9d656ef9bc9e5
Size	3.6 KB
Checksum	sha256:7e5f8ab472f973a38025ba261aa6a997e8851c79d33299f260f9d656ef9bc9e5
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:38:55 (UTC)		1	3.6 KB	-