Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fasta{:bash}
:file
Reference fasta file
*.{fa,fasta,fna}
meta2{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
gtf{:bash}
:file
Reference gtf annotation file
*.{gtf}
meta3{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
splicesites{:bash}
:file
Splices sites in gtf file
*.{txt}
Output
name:type
description
pattern
index{:bash}
meta{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
hisat2{:bash}
:file
HISAT2 genome index file
*.ht2
versions_hisat2{:bash}
${task.process}{:bash}
:string
The name of the process
hisat2{:bash}
:string
The name of the tool
hisat2 --version | sed -n 's/.*version \([^ ]*\).*/\1/p'{:bash}
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
hisat2{:bash}
:string
The name of the tool
hisat2 --version | sed -n 's/.*version \([^ ]*\).*/\1/p'{:bash}
: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.
