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Giovanni Marco Dall'Olio committed a37881a

ADD: documentation on how the output files must be named

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simulations_readme.txt

+A NOTE ON SIMULATION FILE STRUCTURE:
+
+
+The CMS pipeline right now is set up to expect simulations in the following formats: 
+
+Neutral simulations are all in a single directory, and are named according to the following convention:
+
+	bestfit_neutral_params_[iteration number] 
+
+When setting neutralprefix in the parameter files, there is no need to include the underscore between 'params' and [param number].
+
+
+Simulations with selection are in 90 different directories, named param_1 to param_90. Within each directory, there are 100 subdirectories, one for each iteration of the parameter set:
+
+param_1/1
+param_1/2
+...
+param_1/100
+param_2/1
+...
+param_90/100
+
+Within each directory, output for each individual simulation is named according to the following convention: 
+
+	selection_params_[param number]_[iteration number]
+
+When setting selectionprefix in the parameter files, there is no need to include the underscore between 'params' and [param number].
+
+If either of these change, path structures in cms_process_simulations_selection.pl and cms_process_simulations_neutral.pl wll have to be adjusted accordingly. However, because each cosi iteration yields multiple files the folder/subfolder structure is far more efficient than gathering all output in a single directory, and so maintaining it may be a wise idea. 
+
+Additionally, because these simulations are demographically explicit, and following the Schaffner model, population 1 is European-like, population 2 is Asian-like and population 3 is African-like. This is hardcoded into some of the latter scripts in the pipeline, as is the ID of the selected population in the simulations with population-specific selection. If this changes, it will be necessary to edit some of the R scripts called by cms_compute_cms.pl accordingly. 
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