Align RNA-Seq reads to a reference with HISAT2
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
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:‘genome’ ]
index
HISAT2 genome index file
*.ht2
meta3
splicesites
Splices sites in gtf file
*.{txt}
bam
Output BAM file containing read alignments
*.{bam}
summary
Aligment log
*.log
versions
File containing software versions
versions.yml
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.
