Updated Ygor and added protocol #114
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… contains first molgenis-compute protocol
Also restructured params_ok with a for loop and changed summary_count to return a string instead of printing it when encountering an empty VCF file.
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I checked it out and made some tweaks. Sent the changes as a pull request to the MatthieuBeukers:master branch. |
Suggested tweaks for pull request 114.
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Sending some fixes for the commented stuff via pull request to @MatthieuBeukers 's branch.
| #string vbVcfCalls | ||
| #string ygorOutdir | ||
| #string project | ||
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Will need to add a Python module load here.
| #string vbVcfCalls | ||
| #string ygorOutdir | ||
| #string project | ||
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Will need to add a parameter mapping for a Python3 version.
| #string project | ||
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| echo "Compare VaSeBuilder variant calls to gold standard variant calls" | ||
| python "${ygorLocation}" -1 "${vbGoldStandard}" -2 "${$vbVcfCalls}" -o "${ygorOutdir}" -op "${project}" |
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Typo here with the double $:
"${$vbVcfCalls}"
| echo "Comparison to gold standard complete" | ||
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| #SHORT EXPLANATION ON THE DEFINED PARAMETERS | ||
| #ygorLocation = Path to the location of ygor.py tha will perform the comparison |
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| """VCF Comparison Tool. | |||
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I think this blank line is required for typical docstring structure.
| #string ygorLocation | ||
| #string vbGoldStandard | ||
| #string vbVcfCalls | ||
| #string ygorOutdir |
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We can probably use an existing parameter for this one, unless we plan on making a new directory within the CV runs to hold the results.
…ame and recallfile parameters
Please review :)