This workflow uses HISAT2 to map RNA sequencing data to a reference genome.
Usage
You can run the workflow using Cromwell:
java -jar cromwell-<version>.jar run -i inputs.json align-hisat2.wdl
Inputs
Inputs are provided through a JSON file. The minimally required inputs are described below and a template containing all possible inputs can be generated using Womtool as described in the WOMtool documentation.
{
"AlignHisat2.readgroups": "A list of readgroup identifiers, one for each fastq file (pair) provided",
"AlignHisat2.sample": "A sample identifier",
"AlignHisat2.library": "A sequencing library identifier",
"AlignHisat2.outputDir": "The path to the output directory",
"AlignHisat2.inputReads": "A list of fastq pairs (R2 is optional; see the example below) in the same order as the associated readgroup identifiers",
"AlignHisat2.indexFiles": "The path to the HISAT2 index files"
}
Some additional inputs which may be of interest are:
{
"AlignHisat2.platform": "The sequencing platform used, this defaults to 'illumina'",
"AlignHisat2.hisat2.threads": "The number of threads to be used, defaults to 1"
}
Example
{
"AlignHisat2.inputReads": [
{
"R1": "/data/patient1/lane1_R1.fq.gz",
"R2": "/data/patient1/lane1_R2.fq.gz"
},{
"R1": "/data/patient1/lane2_R1.fq.gz",
"R2": "/data/patient1/lane2_R2.fq.gz"
}
],
"AlignHisat2.outputDir": "/mapping/results",
"AlignHisat2.sample": "s1",
"AlignHisat2.library": "lib1",
"AlignHisat2.readgroups": ["lane1", "lane2"],
"AlignHisat2.indexFiles": [
"/hisat2_index/reference.1.ht2",
"/hisat2_index/reference.2.ht2",
"/hisat2_index/reference.3.ht2",
"/hisat2_index/reference.4.ht2",
"/hisat2_index/reference.5.ht2",
"/hisat2_index/reference.6.ht2",
"/hisat2_index/reference.7.ht2",
"/hisat2_index/reference.8.ht2"
],
"AlignHisat2.hisat2.threads": 4
}
output
This workflow produces a directory containing the coordinate-sorted BAM file and its index.