text: user14512: I have a pipeline, which is written in WDL & runs with the help of Cromwell. I use Docker for containerization.
  However, my container is dependent on huge (>100GB databases), which cannot be shipped with the image.
  Is there an option to mount a directory from the host filesystem to a Docker while running Cromwell workflow? I found this functionality in snakemake, therefore I assume it is common, but I haven't found it in the docs yet.
  
  user4413: Not an expert of WDL but looking at Cromwell documentation, there is a block in the configuration of Cromwell called submit-docker:
  
  you'll need to modify the config block
  inside backend.providers in your Cromwell configuration. In
  particular, this block contains a key called submit-docker
  
  In this example file, on line 420, it is possible to specify the mount option which is -v /path/you/need/to/mount:/path/in/docker/container (usually they are the same) to Docker command line. Setting it like that should work.
  
original_text: 14512: <p>I have a pipeline, which is written in <code>WDL</code> &amp; runs with the help of <code>Cromwell</code>. I use <code>Docker</code> for containerization.<br />
  However, my container is dependent on huge (&gt;100GB databases), which cannot be shipped with the image.<br />
  Is there an option to mount a directory from the host filesystem to a <code>Docker</code> while running <code>Cromwell</code> workflow? I found this functionality in <code>snakemake</code>, therefore I assume it is common, but I haven't found it in the docs yet.</p>
   4413: <p>Not an expert of WDL but looking at <a href="https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#configuration-in-detail" rel="nofollow noreferrer">Cromwell documentation</a>, there is a block in the configuration of <code>Cromwell</code> called <code>submit-docker</code>:</p>
  <blockquote>
  <p>you'll need to modify the config block
  inside backend.providers in your Cromwell configuration. In
  particular, this block contains a key called submit-docker</p>
  </blockquote>
  <p>In this <a href="https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/cromwell.examples.conf#L420" rel="nofollow noreferrer">example file</a>, on line <code>420</code>, it is possible to specify the mount option which is <code>-v /path/you/need/to/mount:/path/in/docker/container</code> (usually they are the same) to Docker command line. Setting it like that should work.</p>
  