Description

Extracts ancestrally linked busco genes from a busco full table file.

Input

Name
Description
Pattern

meta (map)

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

fulltable (file)

BUSCO full table tsv file.

*.tsv

meta2 (map)

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

ancestraltable (file)

A reference TSV containing ancestrally linked genes.

*.tsv

Output

Name
Description
Pattern

summary

meta (map)

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

*_summary.tsv (file)

TSV containing a complete summary of results.

dup_location

meta (map)

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

*_duplicated_location.tsv (file)

TSV containing duplicated busco's thought to be ancestrally linked.

comp_location

meta (map)

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

*_complete_location.tsv (file)

TSV containing complete busco's thought to be ancestrally linked.

versions_python

${task.process} (string)

The name of the process

python (string)

The name of the tool

echo \$(python3 --version 2>&1) | sed "s/^.*python //; s/Using.*\$//" (eval)

The expression to obtain the version of the tool

versions_buscopainter

${task.process} (string)

The name of the process

buscopainter.py (string)

The name of the tool

buscopainter.py -v (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

echo \$(python3 --version 2>&1) | sed "s/^.*python //; s/Using.*\$//" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

buscopainter.py (string)

The name of the tool

buscopainter.py -v (eval)

The expression to obtain the version of the tool

Tools

busco_painter Documentation

Scripts to extract ancestrally linked busco genes.

License: GPL v2.0
Pipelines with this module
genomenote
Authors