Description

CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

Sorted BAM/CRAM/SAM file

*.bam

bai{:bash}

:file

Sorted BAM/CRAM/SAM file

*.bam

meta2{:bash}

:map

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

root{:bash}

:file

ROOT file

*.root

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:'test' ]

fasta{:bash}

:file

Path to a directory containing fasta files or a fasta file

*.fa

meta4{:bash}

:map

Groovy Map containing reference information e.g. [ id:'test' ]

fai{:bash}

:file

Path to a fasta file index

*.fai

step{:bash}

:string

One of “his”, “rd”, “call”, “stat”, and “partition”

Output

name:type
description
pattern

root{:bash}

output_meta{:bash}

:map

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

${prefix}.root{:bash}

:file

A ROOT file

*.root

tab{:bash}

output_meta{:bash}

:map

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

${prefix}.tab{:bash}

:file

A tab file containing cnvnator calls

*.tab

versions_cnvnator{:bash}

${task.process}{:bash}

:string

The name of the process

cnvnator{:bash}

:string

The name of the tool

cnvnator 2>&1 | sed -n '3s/CNVnator v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cnvnator{:bash}

:string

The name of the tool

cnvnator 2>&1 | sed -n '3s/CNVnator v//p'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
raredisease
maintainer
Github user ramprasadn
get in touch
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