Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fasta
:file
Reference fasta file
*.{fa,fasta,fna}
gtf
:file
Reference gtf annotation file
*.{gtf}
splicesites
:file
Splices sites in gtf file
*.{txt}
hisat2_memory_input
:string
Memory threshold for HISAT2 index building. When available process memory
meets or exceeds this value, splice sites and exons are used to build a
splice-aware index. Use false to disable splice-aware indexing.
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_hisat2
${task.process}
:string
The name of the process
hisat2
:string
The name of the tool
hisat2 --version | sed -n 's/.*version \([^ ]*\).*/\1/p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
hisat2
:string
The name of the tool
hisat2 --version | sed -n 's/.*version \([^ ]*\).*/\1/p'
:eval
The expression to obtain the version of the tool
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.
