Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
meta2{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
index{:bash}
:file
HISAT2 genome index file
*.ht2
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
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
:file
Output BAM file containing read alignments
*.{bam}
summary{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log{:bash}
:file
Alignment log
*.log
fastq{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*fastq.gz{:bash}
:file
Output FastQ file
*fastq.gz
versions_hisat2{:bash}
${task.process}{:bash}
:string
The name of the process
hisat2{:bash}
:string
The name of the tool
hisat2 --version | sed -n '1s/.*version //p'{:bash}
:eval
The expression to obtain the version of the tool
versions_samtools{:bash}
${task.process}{:bash}
:string
The name of the process
samtools{:bash}
:string
The name of the tool
samtools --version | sed -n '1s/samtools //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 '1s/.*version //p'{:bash}
:eval
The expression to obtain the version of the tool
${task.process}{:bash}
:string
The name of the process
samtools{:bash}
:string
The name of the tool
samtools --version | sed -n '1s/samtools //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.
