modules/cnvpytor_importreaddepth

command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.

read depthcnvcnacall

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

Description

command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.

Input

name:type

description

pattern

`meta`
`:map`

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

`input_file`
`:file`

BAM/CRAM/SAM file

*.{bam,cram}

`index`
`:file`

bam file index

*.{bai,crai}

`meta2`
`:map`

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

`fasta`
`:file`

specifies reference genome file (only for cram file without reference genome)

*.{fasta,fasta.gz,fa,fa.gz}

`fai`
`:file`

Index of reference fasta file

*.fai

Output

name:type

description

pattern

`pytor`

`meta`
`:map`

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

`*.pytor`
`:file`

read depth root file in which read depth data binned to 100 base pair bins will be stored.

*.{pytor}

`versions_cnvpytor`

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

The name of the process

`cnvpytor`
`:string`

The name of the tool

`cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //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

`cnvpytor`
`:string`

The name of the tool

`cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'`
`:eval`

The expression to obtain the version of the tool

Tools

cnvpytor -rd
MIT

calling CNVs using read depth

github.com/abyzovlab/CNVpytor 10.1101/2021.01.27.428472v1

modules/cnvpytor_importreaddepth

Description

Input

`meta`
`:map`

`input_file`
`:file`

`index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

Output

`pytor`

`meta`
`:map`

`*.pytor`
`:file`

`versions_cnvpytor`

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

`cnvpytor`
`:string`

`cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'`
`:eval`

Topics

`versions`

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

`cnvpytor`
`:string`

`cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'`
`:eval`

Tools

cnvpytor -rd
MIT

maintainers

get in touch

modules/cnvpytor_importreaddepth

Description

Input

meta :map

input_file :file

index :file

meta2 :map

fasta :file

fai :file

Output

pytor

meta :map

*.pytor :file

versions_cnvpytor

${task.process} :string

cnvpytor :string

cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p' :eval

Topics

versions

${task.process} :string

cnvpytor :string

cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p' :eval

Tools

cnvpytor -rdMIT

maintainers

get in touch

`meta`
`:map`

`input_file`
`:file`

`index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`pytor`

`meta`
`:map`

`*.pytor`
`:file`

`versions_cnvpytor`

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

`cnvpytor`
`:string`

`cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'`
`:eval`

`versions`

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

`cnvpytor`
`:string`

`cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'`
`:eval`

cnvpytor -rd
MIT