modules/gatk4_splitcram

Splits CRAM files efficiently by taking advantage of their container based structure

cramgatk4splitsplitcram

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/splitcram

Description

Splits CRAM files efficiently by taking advantage of their container based structure

Input

name:type

description

pattern

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`cram{:bash}`
`:file`

The CRAM file to split

*.cram

Output

name:type

description

pattern

`split_crams{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.cram{:bash}`
`:file`

A list of split CRAM files

*.cram

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_splitcram

Description

Input

`meta{:bash}`
`:map`

`cram{:bash}`
`:file`

Output

`split_crams{:bash}`

`meta{:bash}`
`:map`

`*.cram{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

gatk4
Apache-2.0

maintainer

get in touch

modules/gatk4_splitcram

Description

Input

meta{:bash}:map

cram{:bash}:file

Output

split_crams{:bash}

meta{:bash}:map

*.cram{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

gatk4 Apache-2.0

maintainer

get in touch

`meta{:bash}`
`:map`

`cram{:bash}`
`:file`

`split_crams{:bash}`

`meta{:bash}`
`:map`

`*.cram{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

gatk4
Apache-2.0