Creating log files #76
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Ready for your review @standage |
standage
reviewed
Jul 10, 2024
| "WD", | ||
| str(inputfile), |
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I don't understand the significance of this change throughout this test script.
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It was erring out with just using the WD. Really, the input doesn't matter because it's skipping the initial convert step anyway for all of these tests.
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| def create_log(log): | ||
| now = datetime.now() | ||
| dt = now.strftime("%m%d%Y_%H_%M_%S") | ||
| shell("mkdir -p logs/{dt}/input/") | ||
| shell("cp {log} logs/{dt}/strs.log") | ||
| if os.path.isdir(input_name): | ||
| shell("cp {input_name}/* logs/{dt}/input/") | ||
| else: | ||
| shell("cp '{input_name}' logs/{dt}/input/") | ||
| shell("cp snp_config.yaml logs/{dt}/") |
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Is the log argument to this function a path to the Snakemake logfile in $WD/.snakemake/?
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Yes it must be built in.
standage
approved these changes
Jul 10, 2024
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RebJ has requested that lusSTR creates and stores log files. Since snakemake already creates log files but stores them within the
.snakemakedir, I copy those files into a newlogsdirectory within the wd. The log is saved within a dir named with the date and time of the run, creating a new dir for each run. The config file and input file(s) are also copied to this dir (at RebJ's request).