Create SNP workflow #53
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| nofilters: False ##True/False; skip all filtering steps but still creates EFM/STRmix output files | ||
| strand: uas ##uas/forward; strand orientation to report |
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Realized I had never added the argument to specify strand orientation.
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This is a big one @standage but it's ready for your review. I'm not 10000% confident there aren't some bugs in here since it's so much. But I've tried testing it a bunch and satisfied enough that we can merge it and fix any minor bugs we encounter later. |
| lusSTR is able to process SNPs derived from the ForenSeq Signature Prep assay and the ForenSeq Kintelligence assay. SNPs from the ForenSeq Signature Prep assay could be analyzed using either the Verogen UAS or STRait Razor. SNPs from the ForenSeq Kintelligence assay must first be analyzed using the UAS. | ||
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| ### Creating the STR config file |
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Copy/paste error: should be "Creating the SNP config file"
lusSTR/cli/snps.py
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| # ------------------------------------------------------------------------------------------------- | ||
| # Copyright (c) 2020, DHS. | ||
| # | ||
| # This file is part of lusSTR (http://github.com/bioforensics/lusSTR) and is licensed under | ||
| # the BSD license: see LICENSE.txt. |
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Was it intentional to paste this below the placeholder above?
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Ha! I've been scrolled down on this script I've never even realized this was there
| import json | ||
| import os |
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Probably want a header in this file for sake of consistency. DHS copyright claim for this particulay code begins 2023, so that would be the appropriate as the year.
lusSTR/wrappers/snps_format.py
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| # ------------------------------------------------------------------------------------------------- | ||
| # Copyright (c) 2020, DHS. |
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Hair-splitting, but...yeah, 2023 here. 🧐
This PR will convert the old SNP workflow into a snakemake workflow and will likely add some new features along the way!