[BENCHMARK] tool comparison macro benchmarks #156
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Nice work! You already have a nice structure set up, having a separate configuration file and directories for rules and scripts. Might also be good to extract the rules .smk files from /parameter_benchmarks/Snakefile.
I've added some comments, but might have misunderstood your init process :)
| params: | ||
| sample = config["parameters"]["sample"], | ||
| min_qual = config["parameters"]["min_qual"], | ||
| min_var_length = config["parameters"]["min_var_length"], |
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Since the same parameter is used for multiple rules you could define e.g min_var_length globally (before the rules) for the whole .smk file and use it in the shell call as {min_var_length} instead of {params.min_var_length}
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Hmm, I'm not sure, if this makes it more clear. What do you say @joergi-w ?
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I agree with @eaasna that all parameters that are the same in all the rules, should be defined above, so you don't need to repeat them. If it looks too dirty, you can still group them there (but I guess it's fine).
| params: | ||
| sample = config["parameters"]["sample"], | ||
| min_qual = config["parameters"]["min_qual"], | ||
| min_var_length = config["parameters"]["min_var_length"], |
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I agree with @eaasna that all parameters that are the same in all the rules, should be defined above, so you don't need to repeat them. If it looks too dirty, you can still group them there (but I guess it's fine).
…ing_evaluation for a snakemake workflow. Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
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Resolves #123
Our first tool comparison:
CallerComparisonPlot.pdf