modules/fcs_fcsadaptor

Run NCBI’s FCS adaptor on assembled genomes

assemblygenomicsquality controlcontaminationNCBI

https://github.com/nf-core/modules/[...]/modules/nf-core/fcs/fcsadaptor

Description

Run NCBI’s FCS adaptor on assembled genomes

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`assembly:file`

assembly fasta file

Output

name:type

description

pattern

`cleaned_assembly`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`*.cleaned_sequences.fa.gz:file`

Cleaned assembly in fasta format

*.{cleaned_sequences.fa.gz}

`adaptor_report`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`*.fcs_adaptor_report.txt:file`

Report of identified adaptors

*.{fcs_adaptor_report.txt}

`log`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`*.fcs_adaptor.log:file`

Log file

*.{fcs_adaptor.log}

`pipeline_args`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`*.pipeline_args.yaml:file`

Run arguments

*.{pipeline_args.yaml}

`skipped_trims`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`*.skipped_trims.jsonl:file`

Skipped trim information

*.{skipped_trims.jsonl}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

fcs
United States Government Work

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.

ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools github.com/ncbi/fcs/wiki/FCS-adaptor https://github.com/ncbi/fcs

modules/fcs_fcsadaptor

Description

Input

`meta:map`

`assembly:file`

Output

`cleaned_assembly`

`meta:map`

`*.cleaned_sequences.fa.gz:file`

`adaptor_report`

`meta:map`

`*.fcs_adaptor_report.txt:file`

`log`

`meta:map`

`*.fcs_adaptor.log:file`

`pipeline_args`

`meta:map`

`*.pipeline_args.yaml:file`

`skipped_trims`

`meta:map`

`*.skipped_trims.jsonl:file`

`versions`

`versions.yml:file`

Tools

fcs
United States Government Work

maintainers

get in touch

modules/fcs_fcsadaptor

Description

Input

meta:map

assembly:file

Output

cleaned_assembly

meta:map

*.cleaned_sequences.fa.gz:file

adaptor_report

meta:map

*.fcs_adaptor_report.txt:file

log

meta:map

*.fcs_adaptor.log:file

pipeline_args

meta:map

*.pipeline_args.yaml:file

skipped_trims

meta:map

*.skipped_trims.jsonl:file

versions

versions.yml:file

Tools

fcs United States Government Work

maintainers

get in touch

`meta:map`

`assembly:file`

`cleaned_assembly`

`meta:map`

`*.cleaned_sequences.fa.gz:file`

`adaptor_report`

`meta:map`

`*.fcs_adaptor_report.txt:file`

`log`

`meta:map`

`*.fcs_adaptor.log:file`

`pipeline_args`

`meta:map`

`*.pipeline_args.yaml:file`

`skipped_trims`

`meta:map`

`*.skipped_trims.jsonl:file`

`versions`

`versions.yml:file`

fcs
United States Government Work