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`
`:map`

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

`cram`
`:file`

The CRAM file to split

*.cram

Output

name:type

description

pattern

`split_crams`

`meta`
`:map`

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

`*.cram`
`:file`

A list of split CRAM files

*.cram

`versions_gatk4`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

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`
`:map`

`cram`
`:file`

Output

`split_crams`

`meta`
`:map`

`*.cram`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
Apache-2.0

maintainer

get in touch

modules/gatk4_splitcram

Description

Input

meta :map

cram :file

Output

split_crams

meta :map

*.cram :file

versions_gatk4

${task.process} :string

gatk4 :string

gatk --version | sed -n '/GATK.*v/s/.*v//p' :eval

Topics

versions

${task.process} :string

gatk4 :string

gatk --version | sed -n '/GATK.*v/s/.*v//p' :eval

Tools

gatk4Apache-2.0

maintainer

get in touch

`meta`
`:map`

`cram`
`:file`

`split_crams`

`meta`
`:map`

`*.cram`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
Apache-2.0