Description

Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

assembly (file)

assembly fasta file

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

versions (file)

File containing software versions

versions.yml

fcsadaptor_cleaned_assembly (file)

Cleaned assembly in fasta format

*.{cleaned_sequences.fa.gz}

fcsadaptor_report (file)

Report of identified adaptors

*.{fcs_adaptor_report.txt}

fcsadaptor_log (file)

Log file

*.{fcs_adaptor.log}

fcsadaptor_pipeline_args (file)

Run arguments

*.{pipeline_args.yaml}

fcsadaptor_skipped_trims (file)

Skipped trim information

*.{skipped_trims.jsonl}

fcs_gx_report (file)

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)

*.fcs_gx_report.txt

fcsgx_taxonomy_report (file)

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt
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