Description

Run FCS_GX to classify sequences in an assembly, parse the output files into a single CSV.

Input

Name
Description
Pattern

reference (file)

Input fasta reference assembly.

Structure: [ val(meta), path(fasta) ]

*.{fasta,fa,fna}

fcsgx_db (file)

The FSCGX database path

Structure: [ path(directory) ]

ncbi_rankedlineage_path (file)

Path to the rankedlineage.dmp file provided by NCBI taxonomy

Structure: [ path(rankedlineage.dmp) ]

*.{fasta,fa,fna}

Output

Name
Description
Pattern

fcsgxresult (file)

CSV desribing the Structure: [ val(meta), path(csv) ]

*.csv

genomedict (file)

SAMTOOLS dict output

Structure: [ val(meta), path(reference), path(dict) ]

*.fasta | *.dict

fcsgx_report_txt (file)

Classification report from FCSGX

Structure: [ val(meta), path(report) ]

*.fcs_gx_report.txt

fcsgx_taxonomy_rpt (file)

Taxonomy report of classified sequences from FCSGX

Structure: [ val(meta), path(taxonomy_report) ]

*.taxonomy.rpt

Components

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