Description

Converts BED file to contacts BED format using shell utilities.

Input

Name
Description
Pattern

meta (map)

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

file (file)

BED file to convert to contacts format.

*.bed

Output

Name
Description
Pattern

bed

meta (map)

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

*.bed (file)

Contacts BED file generated from the input BED file.

*.bed

versions_gawk

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

gawk --version | grep -o -E "[0-9]+(.[0-9]+)+" | head -n1 (eval)

The expression to obtain the version of the tool

versions_coreutils

${task.process} (string)

The name of the process

coreutils (string)

The name of the tool

ls --version | sed -n "s/ls (GNU coreutils) //p" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

coreutils (string)

The name of the tool

ls --version | sed -n "s/ls (GNU coreutils) //p" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

gawk --version | grep -o -E "[0-9]+(.[0-9]+)+" | head -n1 (eval)

The expression to obtain the version of the tool

Tools

coreutils Documentation

GNU coreutils provides standard utilities such as paste and tr used during conversion.

License: GPL v3.0
Authors