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 reference information
e.g. [ id:‘genome’ ]
index:file
HISAT2 genome index file
*.ht2
meta3:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
splicesites:file
Splices sites in gtf file
*.{txt}
Output
name:type
description
pattern
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.bam:file
Output BAM file containing read alignments
*.{bam}
summary
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.log:file
Aligment log
*.log
fastq
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*fastq.gz:file
Output FastQ file
*fastq.gz
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.
