README update

README.md

@@ -2,6 +2,8 @@
 
 A compilation of scripts and pipelines to count and extract scaffolds of barcodes from linked reads datasets.
 
+**WARNING**: This code is a proof of concept, not a usable software for production. If the code is too slow for your tests or you are encontering some bugs (maybe it's a feature ? :p) don't hesitate to contact us via the issues or with a direct mail to me (yoann [dot] dufresne [at] pasteur [dot] fr).
+
 ## Nomenclature warnings
 During the process of writing a scientific article, some of the datastructure names have been modified.
 In this repository the majority of the names are old names.
@@ -27,6 +29,20 @@ Install the package from the root directory.
 For the majority of the scripts, argparse is used.
 To know how to use it please use the -h command line option.
 
+### Test the complete pipeline on simulated data
+
+For a complete test, we made a bunch of snakemake files.
+If you are looking for a complete pipeline from synthetic data generation, you should look into the "Snakefile_d2_eval" file.
+You can play with the N (number of molecules in the interval graph), M (average number of merge to perform in a barcode), DEV (standard deviation on merge) variables to see impact on performances.
+These values are arrays. You can enter multiple values and all the combinations will be done.
+A summary is output in the tsv file "{WORKDIR}/eval_compare_maxclique.tsv.
+Warning: the pipeline can be very slow for huge number of parameters.
+
+Command to run the pipeline:
+```
+    snakemake -s Snakefile_d2_eval
+```
+
 ### Data simulation
 
 * generate_fake_molecule_graph.py: Create a linear molecule graph, where the molecules are linked to the d molecules on their left and d molecules on their right.

Snakefile_d2_eval

@@ -3,8 +3,8 @@ include: "Snakefile_d2"
 include: "Snakefile_d2_path"
 
 WORKDIR = "snake_experiments" if "workdir" not in config else config["workdir"]
-N = [500]
-D = [6]
+N = [5000]
+D = [10]
 M = [2]
 DEV = [0]