Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

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

meta2{:bash}

:map

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

fasta{:bash}

:file

The fasta reference file.

fai{:bash}

:file

The fasta reference index file.

meta3{:bash}

:map

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

index{:bash}

:file

Chromap genome index files (*.index)

barcodes{:bash}

:file

Cell barcode files

whitelist{:bash}

:file

Cell barcode whitelist file

chr_order{:bash}

:file

Custom chromosome order

pairs_chr_order{:bash}

:file

Natural chromosome order for pairs flipping

Output

name:type
description
pattern

bed{:bash}

meta{:bash}

:map

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

*.bed.gz{:bash}

:file

BED file

*.bed.gz

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

BAM file

*.bam

tagAlign{:bash}

meta{:bash}

:map

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

*.tagAlign.gz{:bash}

:file

tagAlign file

*.tagAlign.gz

pairs{:bash}

meta{:bash}

:map

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

*.pairs.gz{:bash}

:file

pairs file

*.pairs.gz

versions_chromap{:bash}

${task.process}{:bash}

:string

The name of the process

chromap{:bash}

:string

The name of the tool

chromap --version 2>&1{:bash}

:eval

The expression to obtain the version of the tool

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

chromap{:bash}

:string

The name of the tool

chromap --version 2>&1{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools version | sed '1!d;s/.* //'{:bash}

: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
included in
atacseqchipseq
maintainers
Github user mahesh-panchal
Github user joseespinosa
get in touch
Ask a question on Slack Open an issue on GitHub