Here, I'm changing the non-ATRT/non-MB embryonal subtyping module to make sure it uses analysis files data/ (i.e., in the download), rather than files from results. In this case, there were two annotated files from individual CNV callers that are not included in the data download that I've removed. This is because the results were inconclusive, so this seemed like a good way to keep the "always use data/" consistent.
I've uncovered some new issues with CI where we need to skip some chunks. I may not have found all of them quite yet, we'll see if this passes!
Splitting up changes described in https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1399#issuecomment-1124329628.
Here, I'm changing the non-ATRT/non-MB embryonal subtyping module to make sure it uses analysis files
data/(i.e., in the download), rather than files from results. In this case, there were two annotated files from individual CNV callers that are not included in the data download that I've removed. This is because the results were inconclusive, so this seemed like a good way to keep the "always usedata/" consistent.I've uncovered some new issues with CI where we need to skip some chunks. I may not have found all of them quite yet, we'll see if this passes!
Reviewers: Please review the
molecular-subtyping-embryonalmodule inmasterto ensure I didn't miss anything.