Instructions to reproduce GATK variant calling using CWL:

1. Install the specific version of cwltool used in this analysis using pip:

   • pip install cwltool==1.0.20150915034626

2. Download the CWL specifications for tools and workflow along with the JSON file used in the analysis from https://swift.rc.nectar.org.au:8888/v1/AUTH_377/Paper-Data/WorkflowFiles/GATK-CWL-WorkflowFiles.tar.gz. Alternatively these files are provided here as well named as GATK-CWL-WorkflowFiles.tar.gz.

3. Download input data provided and modify the JSON file (GATK-complete-Workflow.json) to add paths for the input, reference sequence (hg19.fasta) and known variant files. Make sure to download the index files (hg19.fasta.*) provided along with the reference sequence and place them in the same directory as hg19.fasta.

4. In addition create a temporary directory (TEMPDIR) in the current working directory which will be used further in the command (as shown in sample command).

5. Run the analysis using the following sample command:

   • cwltool --debug --tmpdir-prefix=PATH_TO/CURRENTDIR/TEMPDIR --tmp-outdir-prefix PATH_TO/CURRENTDIR/TEMPDIR ./GATK-complete-Workflow.cwl ./GATK-complete-Workflow.json

6. The final output of the workflow named as 'CWL-broad-filtered.recode.vcf' is provided for comparisons of results.