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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bed (file)

BED file

*.bed.gz

bam (file)

BAM file

*.bam

tagAlign (file)

tagAlign file

*.tagAlign.gz

pairs (file)

pairs file

*.pairs.gz
included in
atacseq chipseq
maintainers
Github user mahesh-panchal
Github user joseespinosa
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

chromap
GPL v3

Fast alignment and preprocessing of chromatin profiles

github.com/haowenz/chromap