Description

A tool to collect ODB lineages using the GOAT API (with the ENA API as a fallback).

Input

Name
Description
Pattern

meta (map)

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

fasta (file)

Assembly summary file

*.(fasta|fa|fna)$

odb_directory (directory)

Directory containing the ODB lineage data. Do not include the lineage subdirectory.

mapping_directory (directory)

Directory containing the ODB lineage mapping data, these exist as txt files of taxid to lineage.

Output

Name
Description
Pattern

csv

meta (map)

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

*.busco_odb.csv (file)

CSV file containing relevant ODB lineages for the assembly

*.busco_odb.csv

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

versions_get_odb

${task.process} (string)

Name of the process

get_odbs (string)

Name of the tool

get_odbs.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

get_odbs (string)

Name of the tool

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

The expression to obtain the version of the tool

Tools

get_odb Documentation

Generate a CSV containing relevant ODB's to run for a given assembly.

License: MIT
Pipelines with this module
busco
Authors