Description

Parse BUSCO genome-mode full_table.tsv and write three prefixed bedGraph files (Complete, Duplicated, Fragmented), sorted by sequence and numeric start; score is 100.

Input

Name
Description
Pattern

meta (map)

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

full_table (file)

BUSCO full_table.tsv (genome mode)

full_table.tsv

Output

Name
Description
Pattern

versions_pandas

${task.process} (string)

The process the versions were collected from

pandas (string)

The tool name

python -c "import pandas as pd; print(pd.__version__)" (eval)

The expression to obtain the version of the tool

versions_python

${task.process} (string)

The process the versions were collected from

python (string)

The tool name

python -c "import sys; print(sys.version.split()[0])" (eval)

The expression to obtain the version of the tool

complete_bedgraph

meta (map)

Groovy Map containing sample information

*.complete_buscos.bedgraph (file)

Intervals for BUSCO status Complete (sequence, start, end, score)

*.complete_buscos.bedgraph

duplicated_bedgraph

meta (map)

Groovy Map containing sample information

*.duplicated_buscos.bedgraph (file)

Intervals for BUSCO status Duplicated (sequence, start, end, score)

*.duplicated_buscos.bedgraph

fragmented_bedgraph

meta (map)

Groovy Map containing sample information

*.fragmented_buscos.bedgraph (file)

Intervals for BUSCO status Fragmented (sequence, start, end, score)

*.fragmented_buscos.bedgraph

versions_busco_fulltable_to_bedgraph

${task.process} (string)

The process the versions were collected from

busco_fulltable_to_bedgraph.py (string)

The name of the tool

busco_fulltable_to_bedgraph.py --version | sed 's/^.* //' (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

python (string)

The tool name

python -c "import sys; print(sys.version.split()[0])" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

pandas (string)

The tool name

python -c "import pandas as pd; print(pd.__version__)" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

busco_fulltable_to_bedgraph.py (string)

The name of the tool

busco_fulltable_to_bedgraph.py --version | sed 's/^.* //' (eval)

The expression to obtain the version of the tool

Tools

buscofulltabletogenebedgraph Documentation

Convert BUSCO full_table.tsv genomic coordinates into sorted per-status bedGraph files. Output filenames use task.ext.prefix (default meta.id), e.g. sample.complete_buscos.bedgraph.

License: MIT
Authors