modules/chromap_chromap

Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.

chromapalignmentmapfastqbamsamhi-catac-seqchip-seqtrimmingduplicate removal

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

Description

Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.

Input

name:type

description

pattern

`meta`
`:map`

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

`reads`
`:file`

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

`meta2`
`:map`

Groovy Map containing information for the fasta e.g. [ id:‘test’ ]

`fasta`
`:file`

Reference genome FASTA file

*.{fa,fasta,fna}

`fai`
`:file`

Reference genome FASTA index file

*.{fai}

`meta3`
`:map`

Groovy Map containing information for the index e.g. [ id:‘test’ ]

`index`
`:file`

Chromap genome index files (*.index)

`barcodes`
`:file`

Cell barcode files

`whitelist`
`:file`

Cell barcode whitelist file

`chr_order`
`:file`

Custom chromosome order

`pairs_chr_order`
`:file`

Natural chromosome order for pairs flipping

Output

name:type

description

pattern

`bed`

`meta`
`:map`

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

`*.bed.gz`
`:file`

BED file

*.bed.gz

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

BAM file

*.bam

`tagAlign`

`meta`
`:map`

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

`*.tagAlign.gz`
`:file`

tagAlign file

*.tagAlign.gz

`pairs`

`meta`
`:map`

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

`*.pairs.gz`
`:file`

pairs file

*.pairs.gz

`versions_chromap`

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

The name of the process

`chromap`
`:string`

The name of the tool

`chromap --version 2>&1`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`chromap`
`:string`

The name of the tool

`chromap --version 2>&1`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

chromap
GPL v3

Fast alignment and preprocessing of chromatin profiles

github.com/haowenz/chromap

modules/chromap_chromap

Description

Input

meta:map

reads:file

meta2:map

fasta:file

fai:file

meta3:map

index:file

barcodes:file

whitelist:file

chr_order:file

pairs_chr_order:file

Output

bed

meta:map

*.bed.gz:file

bam

meta:map

*.bam:file

tagAlign

meta:map

*.tagAlign.gz:file

pairs

meta:map

*.pairs.gz:file

versions_chromap

${task.process}:string

chromap:string

chromap --version 2>&1:eval

versions_samtools

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Topics

versions

${task.process}:string

chromap:string

chromap --version 2>&1:eval

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Tools

chromap GPL v3

included in

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`meta3`
`:map`

`index`
`:file`

`barcodes`
`:file`

`whitelist`
`:file`

`chr_order`
`:file`

`pairs_chr_order`
`:file`

`bed`

`meta`
`:map`

`*.bed.gz`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`tagAlign`

`meta`
`:map`

`*.tagAlign.gz`
`:file`

`pairs`

`meta`
`:map`

`*.pairs.gz`
`:file`

`versions_chromap`

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

`chromap`
`:string`

`chromap --version 2>&1`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

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

`chromap`
`:string`

`chromap --version 2>&1`
`:eval`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

chromap
GPL v3