Description

Align high throughput chromatin profiles using Chromap then sort with samtools

Input

name
description
pattern

meta

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

ch_reads

Structure: [val(meta), path(reads)]
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

meta2

Groovy Map containing reference information
e.g. [ id:‘test’ ]

ch_index

Structure: [val(meta2), path(index)]
Chromap genome index files

*.index

ch_fasta

Structure: [val(meta2), path(fasta)]
Reference fasta file

*.{fasta,fa}

ch_barcodes

Structure: [path(barcodes)]
Cell barcode files

ch_whitelist

Structure: [path(whitelist)]
Cell barcode whitelist file

ch_chr_order

Structure: [path(chr_order)]
Custom chromosome order

ch_pairs_chr_order

Structure: [path(pairs_chr_order)]
Natural chromosome order for pairs flipping

Output

name
description
pattern

meta

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

bam

BAM file

*.bam

bai

BAM index (currently only for snapaligner)

*.bai

stats

File containing samtools stats output

*.{stats}

flagstat

File containing samtools flagstat output

*.{flagstat}

idxstats

File containing samtools idxstats output

*.{idxstats}

versions

File containing software versions

versions.yml