modules/cnvkit_batch

Copy number variant detection from high-throughput sequencing data

cnvkitbamfastacopy number

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

Description

Copy number variant detection from high-throughput sequencing data

Input

name:type

description

pattern

`meta`
`:map`

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

`tumor`
`:file`

Input tumour sample bam file (or cram)

*.{bam,cram}

`tumor_index`
`:file`

Input tumour sample bam/cram index file (only needed for bam input)

*.{bai,crai}

`normal`
`:file`

Input normal sample bam file (or cram)

*.{bam,cram}

`normal_index`
`:file`

Input normal sample bam/cram index file (only needed for bam input)

*.{bai,crai}

`meta2`
`:map`

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

`fasta`
`:file`

Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)

*.{fa,fasta}

`fasta_fai`
`:file`

Input reference genome fasta index (optional, but recommended for cram_input)

*.{fai}

`meta4`
`:map`

Groovy Map containing information about target file e.g. [ id:‘test’ ]

`targets`
`:file`

Input target bed file

*.{bed}

`meta5`
`:map`

Groovy Map containing information about reference file e.g. [ id:‘test’ ]

`reference`
`:file`

Input reference cnn-file (only for germline and tumor-only running)

*.{cnn}

`panel_of_normals`
`:file`

Input panel of normals file

*.{cnn}

Output

name:type

description

pattern

`bed`

`meta`
`:map`

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

`*.bed`
`:file`

File containing genomic regions

*.{bed}

`cnn`

`meta`
`:map`

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

`*.cnn`
`:file`

File containing coverage information

*.{cnn}

`cnr`

`meta`
`:map`

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

`*.cnr`
`:file`

File containing copy number ratio information

*.{cnr}

`cns`

`meta`
`:map`

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

`*.cns`
`:file`

File containing copy number segment information

*.{cns}

`pdf`

`meta`
`:map`

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

`*.pdf`
`:file`

File with plot of copy numbers or segments on chromosomes

*.{pdf}

`png`

`meta`
`:map`

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

`*.png`
`:file`

File with plot of bin-level log2 coverages and segmentation calls

*.{png}

`versions_cnvkit`

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

The name of the process

`cnvkit`
`:string`

The name of the tool

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`cnvkit`
`:string`

The name of the tool

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

cnvkit
Apache-2.0

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit.readthedocs.io/en/stable

modules/cnvkit_batch

Description

Input

meta:map

tumor:file

tumor_index:file

normal:file

normal_index:file

meta2:map

fasta:file

fasta_fai:file

meta4:map

targets:file

meta5:map

reference:file

panel_of_normals:file

Output

bed

meta:map

*.bed:file

cnn

meta:map

*.cnn:file

cnr

meta:map

*.cnr:file

cns

meta:map

*.cns:file

pdf

meta:map

*.pdf:file

png

meta:map

*.png:file

versions_cnvkit

${task.process}:string

cnvkit:string

cnvkit.py version | sed -e "s/cnvkit v//g":eval

versions_samtools

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Topics

versions

${task.process}:string

cnvkit:string

cnvkit.py version | sed -e "s/cnvkit v//g":eval

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Tools

cnvkit Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`tumor`
`:file`

`tumor_index`
`:file`

`normal`
`:file`

`normal_index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fasta_fai`
`:file`

`meta4`
`:map`

`targets`
`:file`

`meta5`
`:map`

`reference`
`:file`

`panel_of_normals`
`:file`

`bed`

`meta`
`:map`

`*.bed`
`:file`

`cnn`

`meta`
`:map`

`*.cnn`
`:file`

`cnr`

`meta`
`:map`

`*.cnr`
`:file`

`cns`

`meta`
`:map`

`*.cns`
`:file`

`pdf`

`meta`
`:map`

`*.pdf`
`:file`

`png`

`meta`
`:map`

`*.png`
`:file`

`versions_cnvkit`

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

`cnvkit`
`:string`

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

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

`cnvkit`
`:string`

`cnvkit.py version | sed -e "s/cnvkit v//g"`
`:eval`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

cnvkit
Apache-2.0