Description

Builds HISAT2 index for reference genome

Input

name:type
description
pattern

meta:map

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

fasta:file

Reference fasta file

*.{fa,fasta,fna}

meta2:map

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

gtf:file

Reference gtf annotation file

*.{gtf}

meta3:map

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

splicesites:file

Splices sites in gtf file

*.{txt}

Output

name:type
description
pattern

index

meta:map

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

hisat2:file

HISAT2 genome index file

*.ht2

versions

versions.yml:file

File containing software versions

versions.yml

Tools

hisat2
MIT

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.