Description

Determine the chunks to split a CRAM file into for alignment

Input

Name
Description
Pattern

meta (map)

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

cram (file)

Sorted BAM/CRAM/SAM file

*.cram

crai (file)

Cram index file

*.crai

cram_bin_size (integer)

Number of CRAM slices in each CRAM chunk

Output

Name
Description
Pattern

cram_slices

meta (map)

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

cram (file)

Input CRAM file

*.cram

crai (file)

Input CRAM index

*.crai

chunkn (list)

List containing CRAM chunk indexes

slices (list)

List containing the start and end slices of the CRAM chunk

versions_cramchunks

${task.process} (string)

The name of the process

cramchunks (string)

The name of the tool

1.1.0 (string)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

cramchunks (string)

The name of the tool

1.1.0 (string)

The expression to obtain the version of the tool

Tools

cramalign/gencramchunks Documentation

not a real tool!

doi: no DOI available
Pipelines with this module
genomeassemblymetagenomeassembly
Authors