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

The fasta reference file.

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

versions.yml:file

File containing software versions

versions.yml

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