Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-17T11:57:36.313Z
Answers.Text: Thanks, I modified config and was able to mount directories!
Answers.UserDisplayName: crusher083
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-15T23:06:00.910Z
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Body: <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>
  
Tags: <wdl><workflow-management><docker>
Title: Mounting a folder from the host to a Docker, while running it as Cromwell runtime
ThreadText: # Mounting a folder from the host to a Docker, while running it as Cromwell runtime
  
  (Asked by: username_0 on 2022-01-15)
  
  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.
  
  **Tags:** wdl, workflow-management, docker
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-01-15. Score: 1 | Accepted answer
  
  Not an expert of WDL but looking at [Cromwell documentation](https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#configuration-in-detail), 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](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/cromwell.examples.conf#L420), 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.
  
  > **Comments:**
  > **username_0**: Thanks, I modified config and was able to mount directories!  
  
  ---
  
  