modules/fcsgx_rungx

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

genomeassemblycontaminationscreeningcleaningfcs-gx

https://github.com/nf-core/modules/[...]/modules/nf-core/fcsgx/rungx

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`fcsgx_report`

`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.

`taxonomy_report`

`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

`log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.summary.txt`
`:file`

FCSGX log file

*.summary.txt

`hits`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.hits.tsv.gz`
`:file`

Save intermediate alignments

*.hits.tsv.gz

`versions_fcsgx`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

fcsgx
NCBI-PD

The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.

github.com/ncbi/fcs-gx github.com/ncbi/fcs/wiki https://github.com/ncbi/fcs-gx 10.1186/s13059-024-03198-7

modules/fcsgx_rungx

Description

Input

`meta`
`:map`

`taxid`
`:string`

`fasta`
`:file`

`gxdb`
`:directory`

`ramdisk_path`
`:string`

Output

`fcsgx_report`

`meta`
`:map`

`*.fcs_gx_report.txt`
`:file`

`taxonomy_report`

`meta`
`:map`

`*.taxonomy.rpt`
`:file`

`log`

`meta`
`:map`

`*.summary.txt`
`:file`

`hits`

`meta`
`:map`

`*.hits.tsv.gz`
`:file`

`versions_fcsgx`

`${task.process}`
`:string`

`fcsgx`
`:string`

`gx --help | sed '/build/!d; s/.:v//; s/-.//'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`fcsgx`
`:string`

`gx --help | sed '/build/!d; s/.:v//; s/-.//'`
`:eval`

Tools

fcsgx
NCBI-PD

included in

maintainers

get in touch

modules/fcsgx_rungx

Description

Input

meta:map

taxid:string

fasta:file

gxdb:directory

ramdisk_path:string

Output

fcsgx_report

meta:map

*.fcs_gx_report.txt:file

taxonomy_report

meta:map

*.taxonomy.rpt:file

log

meta:map

*.summary.txt:file

hits

meta:map

*.hits.tsv.gz:file

versions_fcsgx

${task.process}:string

fcsgx:string

gx --help | sed '/build/!d; s/.*:v//; s/-.*//':eval

Topics

versions

${task.process}:string

fcsgx:string

gx --help | sed '/build/!d; s/.*:v//; s/-.*//':eval

Tools

fcsgx NCBI-PD

included in

maintainers

get in touch

`meta`
`:map`

`taxid`
`:string`

`fasta`
`:file`

`gxdb`
`:directory`

`ramdisk_path`
`:string`

`fcsgx_report`

`meta`
`:map`

`*.fcs_gx_report.txt`
`:file`

`taxonomy_report`

`meta`
`:map`

`*.taxonomy.rpt`
`:file`

`log`

`meta`
`:map`

`*.summary.txt`
`:file`

`hits`

`meta`
`:map`

`*.hits.tsv.gz`
`:file`

`versions_fcsgx`

`${task.process}`
`:string`

`fcsgx`
`:string`

`gx --help | sed '/build/!d; s/.:v//; s/-.//'`
`:eval`

`versions`

`${task.process}`
`:string`

`fcsgx`
`:string`

`gx --help | sed '/build/!d; s/.:v//; s/-.//'`
`:eval`

fcsgx
NCBI-PD