Description

Create a set of BED files, each describing a chunk of a FASTA

Input

Name
Description
Pattern

meta (map)

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

fai (file)

Sorted BAM/CRAM/SAM file

*.{fai}

chunk_size (integer)

The number of sequences to include per chunk

Output

Name
Description
Pattern

bed

meta (map)

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

*.bed (file)

Sorted BAM/CRAM/SAM file

*.{bed}

versions_gawk

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

gawk -Wversion | sed "1!d; s/.*Awk //; s/,.*//" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

gawk -Wversion | sed "1!d; s/.*Awk //; s/,.*//" (eval)

The expression to obtain the version of the tool

Tools

Pipelines with this module
genomeassembly
Authors