Description

Parses FCS-GX (Fungal Contamination Screening - GX) result files and augments them with NCBI taxonomy lineage information to produce a comprehensive CSV output containing contamination screening results with taxonomic classification.

Input

Name
Description
Pattern

meta (map)

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

taxonomy_report (file)

FCS-GX taxonomy report file

*.taxonomy.rpt

meta2 (map)

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

fcs_report (file)

FCS-GX report file

*.fcs_gx_report.txt

ncbi_rankedlineage_path (file)

NCBI rankedlineage.dmp file

*rankedlineage*

Output

Name
Description
Pattern

fcsgxresult

meta (map)

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

*_parsed_fcsgx.csv (file)

Parsed FCS-GX results with NCBI taxonomy lineage information in CSV format

versions_python

${task.process} (string)

The name of the process

python (string)

The name of the tool

python --version | sed "s/Python //" (eval)

The expression to obtain the version of the tool

versions_parsefcsgx

${task.process} (string)

The name of the process

parse_fcsgx_result (string)

The name of the tool

parse_fcsgx_result.py --version (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

python (string)

The name of the tool

python --version | sed "s/Python //" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

parse_fcsgx_result (string)

The name of the tool

parse_fcsgx_result.py --version (eval)

The expression to obtain the version of the tool

Tools

parse_fcsgx_result Documentation

Parse FCS-GX result files and augment with NCBI taxonomy lineage information

doi: no DOI availableLicense: MIT
Authors