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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Update focal-cn-preparation to use consensus SEG file in data download #1130

Closed jaclyn-taroni closed 3 years ago

jaclyn-taroni commented 3 years ago

The focal-cn-preparation module was taking over an hour to run in CI. This is because it was using the consensus SEG file that is committed to the repository, which is not for a subset of samples but instead contains all samples. With the release of v20, there's no reason to continue to use the file in analyses/copy_number_consensus_call/results so here I am changing the path in the second notebook of focal-cn-preparation to use the file in the data download. In the context of CI, this will be the subset file.

Closes #1129.

jaclyn-taroni commented 3 years ago

I'm not going to update the HTML for this notebook, because I expect that will happen as part of getting #1124 through anyway.

jaclyn-taroni commented 3 years ago

It is curious, though, that the consensus CN steps happens right before this one and I would expect then that the file in results for that module would then be from the subset of samples. There might be something snakemake-y happening that I don't understand.

jaclyn-taroni commented 3 years ago

Closing in favor of #1124