Description

A tool to filter an assembly fasta based on FCSGX and TIARA summary files. This also generates a join FCSGX/TIARA summary file.

Input

Name
Description
Pattern

meta (map)

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

fai (file)

Assembly reference fai file

*.fai$

tiara_meta (map)

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

tiara_txt (file)

Assembly summary file from Tiara

*.txt$

fcs_meta (map)

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

fcs_csv (file)

Assembly summary file, a parsed fcsgx output file.

*.csv$

taxid (integer)

NCBI Taxonomy ID of the assembly.

ncbi_rankedlineage (file)

File containing the NCBI ranked lineage data.

Output

Name
Description
Pattern

keep_scaffs

meta (map)

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

*_autofiltered.txt (file)

A TXT file of clean scaffold headers, deemed safe by FCSGX and Tiara analysis.

*_autofiltered.txt

versions_python

${task.process} (string)

Name of the process

python (string)

Name of the tool

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

The expression to obtain the version of the tool

remove_scaffolds

meta (map)

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

*_removed_scaffolds.txt (file)

TXT file of scaffold names filtered out by by FCSGX and Tiara analysis.

*_removed_scaffolds.txt

fcs_tiara_summary

meta (map)

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

*_ABNORMAL_CHECK.csv (file)

CSV file containing information about abnormal contamination in files and how they now labeled.

*_ABNORMAL_CHECK.csv

versions_autofilter

${task.process} (string)

Name of the process

autofilter (string)

Name of the tool

autofilter.py --version | cut -d" " -f2 (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

Name of the process

python (string)

Name of the tool

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

The expression to obtain the version of the tool

${task.process} (string)

Name of the process

autofilter (string)

Name of the tool

autofilter.py --version | cut -d" " -f2 (eval)

The expression to obtain the version of the tool

Tools

autofilter Documentation

Filter an assembly with FCSGX and TIARA summary files.

License: MIT
Authors