BioWDL: aligning

A collection of BioWDL workflows for aligning sequencing data.

Please be aware that the page you are currently viewing is not for the latest available version!

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. See this page for some additional general notes and information about pipeline inputs.

{
  "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.starIndexDir": "The path to the STAR index"
}

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.starIndexDir": "/home/user/genomes/human/star",
  "AlignStar.star.runThreadN": "The number of threads to be used, defaults to 1",
}

output

This workflow produces a directory containing the STAR output, including a coordinate-sorted BAM file and its index.