This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Automation beyond cromwell
Background: I work in food safety, and we type our isolates using MLST, and then perform a SNP analysis within each sequence type to determine whether we have related isolates. For the SNPs analysis, we also include restrospective isolates with that Sequence Type we found previously.
I am looking for a way to automate this process. Right now, it's quite a lot of work to extract all isolates with a certain Sequence Type, get the appropriate reference, run the
wdltool inputs, make sure all settings are correct, and run cromwell. And then once we get new data, we have to do it all over again with one (or more) additional sample(s). Of course call caching helps with the computational time, but not with the 'manual' time we have to spent setting up each analysis.
Are there any tools available that can help queue up cromwell runs for each MLST type? I imagine re-running a data set with one extra sample is something that is pretty common.