modules/pairtools_parse

Find ligation junctions in .sam, make .pairs

ligation junctionsparsepairtools

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

Description

Find ligation junctions in .sam, make .pairs

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`chromsizes`
`:file`

chromosome size file

Output

name:type

description

pattern

`pairsam`

`meta`
`:map`

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

`*.pairsam.gz`
`:file`

parsed pair file

*.{pairsam.gz}

`stat`

`meta`
`:map`

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

`*.pairsam.stat`
`:file`

stats of the pairs

*.{pairsam.stat}

`versions_pairtools`

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

The name of the process

`pairtools`
`:string`

The name of the tool

`pairtools --version | sed 's/.pairtools.version //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`pairtools`
`:string`

The name of the tool

`pairtools --version | sed 's/.pairtools.version //'`
`:eval`

The expression to obtain the version of the tool

Tools

pairtools
MIT

CLI tools to process mapped Hi-C data

http://pairtools.readthedocs.io https://github.com/mirnylab/pairtools

modules/pairtools_parse

Description

Input

`meta`
`:map`

`bam`
`:file`

`chromsizes`
`:file`

Output

`pairsam`

`meta`
`:map`

`*.pairsam.gz`
`:file`

`stat`

`meta`
`:map`

`*.pairsam.stat`
`:file`

`versions_pairtools`

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

`pairtools`
`:string`

`pairtools --version | sed 's/.pairtools.version //'`
`:eval`

Topics

`versions`

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

`pairtools`
`:string`

`pairtools --version | sed 's/.pairtools.version //'`
`:eval`

Tools

pairtools
MIT

included in

maintainer

get in touch

modules/pairtools_parse

Description

Input

meta:map

bam:file

chromsizes:file

Output

pairsam

meta:map

*.pairsam.gz:file

stat

meta:map

*.pairsam.stat:file

versions_pairtools

${task.process}:string

pairtools:string

pairtools --version | sed 's/.*pairtools.*version //':eval

Topics

versions

${task.process}:string

pairtools:string

pairtools --version | sed 's/.*pairtools.*version //':eval

Tools

pairtools MIT

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`chromsizes`
`:file`

`pairsam`

`meta`
`:map`

`*.pairsam.gz`
`:file`

`stat`

`meta`
`:map`

`*.pairsam.stat`
`:file`

`versions_pairtools`

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

`pairtools`
`:string`

`pairtools --version | sed 's/.pairtools.version //'`
`:eval`

`versions`

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

`pairtools`
`:string`

`pairtools --version | sed 's/.pairtools.version //'`
`:eval`

pairtools
MIT