Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

meta2 (map)

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

meta3 (map)

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

meta4 (map)

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

bam (file)

Sorted BAM/CRAM/SAM file

*.bam

bai (file)

Sorted BAM/CRAM/SAM file

*.bam

root (file)

ROOT file

*.root

fasta (file)

Path to a directory containing fasta files or a fasta file

*.fa

fai (file)

Path to a fasta file index

*.fai

Output

Name (Type)
Description
Pattern

output_meta (map)

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

versions (file)

File containing software versions

versions.yml

root (file)

A ROOT file

*.root

tab (file)

A tab file containing cnvnator calls

*.tab