modules/bedtools_complement

Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

bedgffvcfcomplementbedtoolsintervals

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

Description

Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

Input

name:type

description

pattern

`meta:map`

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

`bed:file`

Input BED file

*.{bed}

`sizes:file`

File which defines the chromosome lengths for a given genome

*.{sizes}

Output

name:type

description

pattern

`bed`

`meta:map`

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

`*.bed:file`

Bed file with all genomic intervals that are not covered by at least one record from the input file.

*.{bed}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

bedtools
MIT

A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.

bedtools.readthedocs.io/en/latest/content/tools/complement

modules/bedtools_complement

Description

Input

meta:map

bed:file

sizes:file

Output

bed

meta:map

*.bed:file

versions

versions.yml:file

Tools

bedtools MIT

`meta:map`

`bed:file`

`sizes:file`

`bed`

`meta:map`

`*.bed:file`

`versions`

`versions.yml:file`

bedtools
MIT