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This workflow uses STAR 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-star.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.
{
"AlignStar.readgroups": "A list of readgroup identifiers, one for each fastq file (pair) provided",
"AlignStar.sample": "A sample identifier",
"AlignStar.library": "A sequencing library identifier",
"AlignStar.outputDir": "The path to the output directory",
"AlignStar.inputR1": "A list of first-end fastq files (in the same order as the associated readgroup identifiers)",
"AlignStar.inputR2": "A list of second-end fastq files (in the same order as the associated readgroup identifiers). This input may be ignored for single-end sequencing experiments",
"AlignStar.indexFiles": "The paths to the STAR index files."
}
Some additional inputs which may be of interest are:
{
"AlignStar.platform": "The sequencing platform used, this defaults to 'illumina'",
"AlignStar.star.runThreadN": "The number of threads to be used, defaults to 1",
"AlignStar.star.twopassMode": "The two-pass mode to be used (if any)"
}
Example
{
"AlignStar.readgroups": [
"lane1",
"lane2"
],
"AlignStar.sample": "s1",
"AlignStar.library": "lib1",
"AlignStar.outputDir": "/home/user/mapping/results",
"AlignStar.inputR1": [
"/home/user/data/patient1/lane1_R1.fq.gz",
"/home/user/data/patient1/lane2_R1.fq.gz"
],
"AlignStar.inputR2": [
"/home/user/data/patient1/lane1_R2.fq.gz",
"/home/user/data/patient1/lane2_R2.fq.gz"
],
"AlignStar.indexFiles": [
"/star_index/chrLength.txt",
"/star_index/chrName.txt",
"/star_index/chrNameLength.txt",
"/star_index/chrStart.txt",
"/star_index/Genome",
"/star_index/genomeParameters.txt",
"/star_index/SA",
"/star_index/SAindex"
],
"AlignStar.star.runThreadN": 4
}
output
This workflow produces a directory containing the STAR output, including a coordinate-sorted BAM file and its index.