fastq_align_chromap

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

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

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

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

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

Structure: [path(barcodes)]
Cell barcode files

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

Structure: [path(chr_order)]
Custom chromosome order

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

Boolean controling whether the readgroups should be added or updated
after chromap alignment