Running WDL pipeline on public Bam file from ISB-CGC

This workflow gathers GC content from a BAM file (or a list of BAM files) to a text file.


  • Java
  • Graphviz
  • Docker
  • Gcsfuse
  • WDL (Cromwell and Womtool)
  • A public bam file from ISB-CGC at the address: gs://gdc-ccle-open/692a845c-7957-41f2-b679-5434c69ba25b/G27328.Calu-6.1.bam

To install Java, Docker, Graphviz and WDL, see our VM Workflow Tools Installation Cheatsheet for instructions. To set up gcsfuse in order to get access to the BAM file, please visit Running Workflow with GCSFUSE.


The requirements above are crucial to running this workflow. Please make sure you have them installed properly prior to running this workflow.

Installing Cromwell and Womtool:

Download the cromwell-XY.jar and womtool-XY.jar at to your local machine


“XY” in cromwell-XY.jar and womtool-XY.jar is the version of the software. At the time of this tutorial, the latest version is “51”. For all the code from here “XY” will be “51” e.g. cromwell-XY.jar becomes cromwell-51.jar. Please change the code accordingly to reflect the version that you have.

Example using Wget:

$ wget
$ wget

Download this tutorial:

$ sudo add-apt-repository universe
$ sudo apt update
$ sudo apt install subversion

#cloning this tutorial
$ svn checkout

Running WDL

You should have a WDL-GCgather directory with 3 files inside. to simplify the command, I will move the cromwell-51.jar and womtool-51.jar into the WDL-GCgather* directory:

$ mv *-51.jar WDL-GCgather/

We are going to change the address in bamfiles.txt file to the one you created in the Running Workflow with GCSFUSE tutorial

#go into the folder
$ cd WDL-GCgather
$ nano bamfiles.txt

At the top of the file you will see this:

/home/thinh_vo/testGcsfuse/G27328.Calu-6.1.bam        bam1

Replace “/home/thinh_vo/testGcsfuse/G27328.Calu-6.1.bam” with your new address from the gcsfuse tutorial for example: “/home/thinh_vo/testGcsfuse/G27328.Calu-6.1.bam”. Now the script is ready to run with WDL. Save the change, then run the script with this command:

$ java -jar cromwell-51.jar run gcstats.wdl -i gcstats.inputs


This Bam file is quite large, it may take about 15 mins ~ 20 mins to run. Also make sure you have installed Java.

Once the Cromwell finished, the result will be located inside the folder called cromwell-executions (also they will announce right before they stop running where the output is (see image below))

It should look like this, the final_gc_stats_out.txt is the final output of this workflow :

../../_images/RunningWDLWithBam_4.png ../../_images/RunningWDLWithBam_3.png

Creating visualization with Womtool

Run this command:

$ java -jar womtool-51.jar graph gcstats.wdl | dot -Tpng > visual.png

A file named “visual.png” will be created and ready to be downloaded

It should look like this:


To see the result of this workflow, you can check it here.

Have feedback or corrections? Please email us at