implements a script that 1) filters loci not in FINNGEN out of top report and 2) filters out loci that are near strong hits
implements a script that calculates LD between loci in top reports, and checks whether the loci are the storngest hits in their region.
Adds these to the docker image
Adds these scripts to the WDL
Refactors the WDL
Before this PR, the WDL outputs were just globbed from the tasks. As long as the task did not fail, you got either 0 or 4 files, depending on whether there were results for that phenotype. Now, since there are other downstream tasks using those files, those files have to exist. Optional outputs are only supported by WDL 1.1, so I can't use that. Instead I use a boolean flag for whether there are results and using that to determine whether downstream tasks are performed. To include only successful results to outputs, there is an extra task outputter for separating the correct outputs - This is not ideal, maybe this can be replaced with something a bit better?
This PR does the following things:
Before this PR, the WDL outputs were just globbed from the tasks. As long as the task did not fail, you got either 0 or 4 files, depending on whether there were results for that phenotype. Now, since there are other downstream tasks using those files, those files have to exist. Optional outputs are only supported by WDL 1.1, so I can't use that. Instead I use a boolean flag for whether there are results and using that to determine whether downstream tasks are performed. To include only successful results to outputs, there is an extra task outputter for separating the correct outputs - This is not ideal, maybe this can be replaced with something a bit better?
This is still a draft, input is very welcome!