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Fix CNV conensus call workflow #984
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kgaonkar6
approved these changes
Apr 5, 2021
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Purpose/implementation Section
What scientific question is your analysis addressing?
In #964 (comment) @kgaonkar6 ran into some trouble with the CNV consensus workflow, and specifically the merge step. I confirmed the bug, and guessed that it might be due to the very long list of arguments to
catin that step of the workflow.What was your approach?
To address the error, I converted the
merge_allstep to use a python loop and append to the output file rather than trying to pass the long file list to the shell. This seemed to solve the problem. It is probably a bit less efficient, but definitely not anything noticeable in the workflow as a whole.Results did not change, except for a single small ordering change on one line (not sure why that happened, but the new order is actually in order, so 🤷🏼).
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Confirm that this fixes the bug for others, not just me.
Is there anything that you want to discuss further?
If it works, I don't think so!