nf-core/fcs/fcsgx @ 0.0.0-6c4ed3a
Summary
Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.
Get started
Add the following snippet to your workflow script to include this module.
include { FCS_FCSGX } from 'nf-core/fcs/fcsgx'
License
MIT License
Process
Name
|
FCS_FCSGX |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', taxid:'6973' ] |
|---|---|
assembly
file
|
assembly fasta file |
gxdb
file
|
The NCBI GenBank database to search against. |
|---|
Output
3 channels
#1
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
#2
fcs_gx_report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', taxid:'9606' ] |
|---|---|
out/*.fcs_gx_report.txt
file
|
Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW) *.fcs_gx_report.txt
|
#3
taxonomy_report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', taxid:'9606' ] |
|---|---|
out/*.taxonomy.rpt
file
|
Report containing the contig identifier and mapped contaminant species *.taxonomy.rpt
|
| 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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:17:04 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Ffcs%2Ffcsgx/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/fcs/fcsgx/blobs/sha256:fcfd89cb50baa7e2bc84b008357fb3d63fc2e31c5b5875c9edd9ad16b4ce0fef |
| Size | 2.5 KB |
| Checksum | sha256:fcfd89cb50baa7e2bc84b008357fb3d63fc2e31c5b5875c9edd9ad16b4ce0fef |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:17:04 (UTC) | 4 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:00:42 (UTC) | 3 | 2.5 KB |