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Make sure non-ATRT/non-MB embryonal subtyping module uses data download #1415
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Rip out other sex chromosome files not included in data download
Also rerun
This was referenced May 19, 2022
Merged
sjspielman
approved these changes
May 20, 2022
| @@ -106,7 +125,7 @@ histologies_df <- read_tsv(histologies_file, | |||
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| # copy number consensus file (analysis file) | |||
| # TODO: get this from data download | |||
| cn_consensus_seg <- file.path("..", "copy_number_consensus_call", "results", | |||
| cn_consensus_seg <- file.path(data_dir, | |||
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Splitting up changes described in #1399 (comment).
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.