modules/cnvnator_cnvnator

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

cnvnatorcnvcna

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

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 ]

`bam`
`:file`

Sorted BAM/CRAM/SAM file

*.bam

`bai`
`:file`

Sorted BAM/CRAM/SAM file

*.bam

`meta2`
`:map`

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

`root`
`:file`

ROOT file

*.root

`meta3`
`:map`

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

`fasta`
`:file`

Path to a directory containing fasta files or a fasta file

*.fa

`meta4`
`:map`

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

`fai`
`:file`

Path to a fasta file index

*.fai

`step`
`:string`

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

Output

name:type

description

pattern

`root`

`output_meta`
`:map`

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

`${prefix}.root`
`:file`

A ROOT file

*.root

`tab`

`output_meta`
`:map`

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

`${prefix}.tab`
`:file`

A tab file containing cnvnator calls

*.tab

`versions_cnvnator`

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

The name of the process

`cnvnator`
`:string`

The name of the tool

`cnvnator 2>&1 | sed -n '3s/CNVnator 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

`cnvnator`
`:string`

The name of the tool

`cnvnator 2>&1 | sed -n '3s/CNVnator v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

cnvnator
MIT

Tool for calling copy number variations.

github.com/abyzovlab/CNVnator github.com/abyzovlab/CNVnator/blob/master/README.md https://github.com/abyzovlab/CNVnator

modules/cnvnator_cnvnator

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`root`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

`step`
`:string`

Output

`root`

`output_meta`
`:map`

`${prefix}.root`
`:file`

`tab`

`output_meta`
`:map`

`${prefix}.tab`
`:file`

`versions_cnvnator`

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

`cnvnator`
`:string`

`cnvnator 2>&1 | sed -n '3s/CNVnator v//p'`
`:eval`

Topics

`versions`

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

`cnvnator`
`:string`

`cnvnator 2>&1 | sed -n '3s/CNVnator v//p'`
`:eval`

Tools

cnvnator
MIT

included in

maintainer

get in touch

modules/cnvnator_cnvnator

Description

Input

meta:map

bam:file

bai:file

meta2:map

root:file

meta3:map

fasta:file

meta4:map

fai:file

step:string

Output

root

output_meta:map

${prefix}.root:file

tab

output_meta:map

${prefix}.tab:file

versions_cnvnator

${task.process}:string

cnvnator:string

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

Topics

versions

${task.process}:string

cnvnator:string

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

Tools

cnvnator MIT

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`root`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

`step`
`:string`

`root`

`output_meta`
`:map`

`${prefix}.root`
`:file`

`tab`

`output_meta`
`:map`

`${prefix}.tab`
`:file`

`versions_cnvnator`

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

`cnvnator`
`:string`

`cnvnator 2>&1 | sed -n '3s/CNVnator v//p'`
`:eval`

`versions`

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

`cnvnator`
`:string`

`cnvnator 2>&1 | sed -n '3s/CNVnator v//p'`
`:eval`

cnvnator
MIT