modules/pretextmap

converts sam/bam/cram/pairs into genome contact map

contactbammap

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

Description

converts sam/bam/cram/pairs into genome contact map

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM/SAM file or pairs formatted reads file

*.{bam,cram,sam,pairs.gz}

`meta2`
`:map`

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

`fasta`
`:file`

Reference sequence file

*.{fasta,fna,fa}

`fai`
`:file`

Reference sequence index file

*.{fai}

Output

name:type

description

pattern

`pretext`

`meta`
`:map`

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

`*.pretext`
`:file`

pretext map

*.pretext

`versions_pretextmap`

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

Name of the process

`PretextMap`
`:string`

Name of the tool

`PretextMap | sed "/Version/!d; s/.*Version //"`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

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

Name of the process

`samtools`
`:string`

Name of the tool

`samtools --version | sed "1!d; s/samtools //"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

Name of the process

`PretextMap`
`:string`

Name of the tool

`PretextMap | sed "/Version/!d; s/.*Version //"`
`:eval`

The expression to obtain the version of the tool

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

Name of the process

`samtools`
`:string`

Name of the tool

`samtools --version | sed "1!d; s/samtools //"`
`:eval`

The expression to obtain the version of the tool

Tools

pretextmap
MIT

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

github.com/wtsi-hpag/PretextMap github.com/wtsi-hpag/PretextMap/blob/master/README.md

modules/pretextmap

Description

Input

`meta`
`:map`

`input`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

Output

`pretext`

`meta`
`:map`

`*.pretext`
`:file`

`versions_pretextmap`

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

`PretextMap`
`:string`

`PretextMap | sed "/Version/!d; s/.*Version //"`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools --version | sed "1!d; s/samtools //"`
`:eval`

Topics

`versions`

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

`PretextMap`
`:string`

`PretextMap | sed "/Version/!d; s/.*Version //"`
`:eval`

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

`samtools`
`:string`

`samtools --version | sed "1!d; s/samtools //"`
`:eval`

Tools

pretextmap
MIT

maintainers

get in touch

modules/pretextmap

Description

Input

meta :map

input :file

meta2 :map

fasta :file

fai :file

Output

pretext

meta :map

*.pretext :file

versions_pretextmap

${task.process} :string

PretextMap :string

PretextMap | sed "/Version/!d; s/.*Version //" :eval

versions_samtools

${task.process} :string

samtools :string

samtools --version | sed "1!d; s/samtools //" :eval

Topics

versions

${task.process} :string

PretextMap :string

PretextMap | sed "/Version/!d; s/.*Version //" :eval

${task.process} :string

samtools :string

samtools --version | sed "1!d; s/samtools //" :eval

Tools

pretextmapMIT

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`pretext`

`meta`
`:map`

`*.pretext`
`:file`

`versions_pretextmap`

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

`PretextMap`
`:string`

`PretextMap | sed "/Version/!d; s/.*Version //"`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools --version | sed "1!d; s/samtools //"`
`:eval`

`versions`

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

`PretextMap`
`:string`

`PretextMap | sed "/Version/!d; s/.*Version //"`
`:eval`

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

`samtools`
`:string`

`samtools --version | sed "1!d; s/samtools //"`
`:eval`

pretextmap
MIT