How to run this pipeline in one go?

[nikhilp11]

When I run docker run duplexa/4dn-hic:v43 it gives me a list of all the scripts.
How do I run the whole pipeline at once?
Do I have to run each script individually?

[clarabakker]

Hi Nikhil,

Yes, the command you used runs the docker container, rather than the pipeline. The docker default command for this image simply provides a list of the scripts. You can enter the docker container and run scripts by running docker run duplexa/4dn-hic:v43 /bin/bash (or of course provide other arguments after the image name).

You can reference the cwl files to understand how each script is used and its ordering. All the individual cwls are grouped into three steps, each with its own cwl (bwa-mem.cwl, hi-c-processing-bam.cwl, and hi-c-processing-pairs.cwl). Here's the READme for running CWLs. In short, we use a cwl runner for this purpose, which you can also do if you would like.

Best wishes!