modules/bedtools_multiinter

Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.

bedtoolsmultintervalbedvcfgff

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

Description

Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`beds{:bash}`
`:list`

List of files to be merged

*.{bed,vcf,gff}

`chrom_sizes{:bash}`
`:file`

Chromosome sizes file

*{.sizes,.txt}

Output

name:type

description

pattern

`bed{:bash}`

`meta{:bash}`
`:map`

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

`*.bed{:bash}`
`:file`

Common interval bed

*.{bed}

`versions{:bash}`

`versions.yml{:bash}`
`: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/multiinter

modules/bedtools_multiinter

Description

Input

`meta{:bash}`
`:map`

`beds{:bash}`
`:list`

`chrom_sizes{:bash}`
`:file`

Output

`bed{:bash}`

`meta{:bash}`
`:map`

`*.bed{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

bedtools
MIT

maintainer

get in touch

modules/bedtools_multiinter

Description

Input

meta{:bash}:map

beds{:bash}:list

chrom_sizes{:bash}:file

Output

bed{:bash}

meta{:bash}:map

*.bed{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

bedtools MIT

maintainer

get in touch

`meta{:bash}`
`:map`

`beds{:bash}`
`:list`

`chrom_sizes{:bash}`
`:file`

`bed{:bash}`

`meta{:bash}`
`:map`

`*.bed{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

bedtools
MIT