Feature/traceback concat #29
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✔️ added contribution guidelines ✔️ remove some unnecessary files ✔️ cleanup README
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| # Contributing to Post-Processing | |||
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Hi Eric, I followed these commands when working on the remove_variants_by_annotations.py conversion to a subcommand and was able to understand the instructions clearly. Great job on explaining the steps/resources needed to set up these commands!
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| ### VarDictJava | ||
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| The sub-command `pv vardict` allows users to perform post-processing on VarDictJava output. The two supported inputs to `pv vardict` from VarDictJava are `single` and `case-control` vcfs. |
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very minor change, but I'd recommend adding the version of VarDictJava in the README. mostly due to the fact that the docker image created for VarDict that is compatible with M1 is version 1.8.2 (same version used by MSK), but the version used by nf-core is 1.8.3
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good call. I added the version in the docs/VARDICT.md and added a link in the README.
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| ### Maf | ||
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| maf concat examples: |
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again very minor, but maybe adding a sentence at the beginning of the README (similar to line 10) with a quick explanation to what the category of 'maf' commands are intended to do in post-processing. When the vcf2maf module has been approved in msk-modules, we could even add a hyperlink to it in the README here
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similar to above I added a link to the README that points to docs/maf
| mafa = MAFFile(maf, separator) | ||
| mafa = mafa.tag("common_variant") | ||
| mafa.to_csv(f"{output_maf}".format(outputFile=output_maf), index=False, sep="\t") | ||
| return 0 |
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Not a review comment but a question-- I noticed you return "0" at the end of your sub-command functions. What is the purpose of returning 0 as compared to a string value indicating the execution of the sub-command has completed or not returning anything at all?
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In python, if I'm writing a file in a function as opposed to returning something, I still like to return a 0 to indicate a successful run of the function. Some languages like C require you return something at the completion of a function. It's not required in python, but something I think is decent style. We can change the return as well.
pv maf concatto match new file - operation standards