If I'm not wrong, all the examples I saw so far with WDL require to pull the tools from docker. If my needs are only limited to the tools from the "swiss army knife" app, is there a way to run a WDL workflow using those "local" tools ?
(context: my needs are currently quite simple and my cluster/sysadmin doesn't support docker)
Alternatively, you can build the workflow using UI. Then you can use dx get <workflow-id> to get the code of your workflow, so you can keep the code, modify it if needed, and dx build the workflow back to the platform in the future. I personally found this easier and reasonable level of reproducibility.
Thanks for your anwers. Based on your answers for my other questions, I'll first have a look at the nextflow importer before trying to do anything with WDL.
As another alternative for developing a WDL workflow - if cannot run docker on your machine - you can run a UKB RAP cloud worker app, such ttyd or cloud workstation and compile your WDL workflow there. Docker is already part of it, so you do not need to install it. You will just need to install prerequisities for WDL (maybe Java, dxCompiler itself etc.). Advantage of this approach would be that once your WDL code is compiled and converted into a DNAnexus UKB RAP applet, it is available in your project, therefore you could run it via GUI, CLI or dxpy.
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Alternatively, you can build the workflow using UI. Then you can use dx get <workflow-id> to get the code of your workflow, so you can keep the code, modify it if needed, and dx build the workflow back to the platform in the future. I personally found this easier and reasonable level of reproducibility.
My grad school blocks Docker too.
It's possible to run WDL with app or applet that is not Docker base on DNAnexus.
You can see the tutorial here https://youtu.be/vyzYChm0e1g?t=573
Thanks for your anwers. Based on your answers for my other questions, I'll first have a look at the nextflow importer before trying to do anything with WDL.
As another alternative for developing a WDL workflow - if cannot run docker on your machine - you can run a UKB RAP cloud worker app, such ttyd or cloud workstation and compile your WDL workflow there. Docker is already part of it, so you do not need to install it. You will just need to install prerequisities for WDL (maybe Java, dxCompiler itself etc.). Advantage of this approach would be that once your WDL code is compiled and converted into a DNAnexus UKB RAP applet, it is available in your project, therefore you could run it via GUI, CLI or dxpy.
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