chore(main): Update config/README.md

Author: fcaretti

Diff for: config/README.md

@@ -1,5 +1,18 @@
-Describe how to configure the workflow (using config.yaml and maybe additional files).
-All of them need to be present with example entries inside of the config folder.
-
-In config/config.yml:
-* Add the name of the folder containing the bamfiles under data/folder
+The starting point of the pipeline are .bam files from one or more RNA samples. They are assumed to have been already sequenced.
+Edit the config/config.yml file as follows:
+* data:
+    1) ["folder"]: path to the folder containing the .bam files
+* reference:
+    1) ["folder"]: the folder containing the .fa file
+    2) ["genome"]: the genome file
+* known_sites: used only in FreeBayes, and not GATK's HaplotypeCaller. Currently not used
+* filtering:
+    1) ["params"]: the parameters for bcftools filter. An example is provided
+* vep:
+    1) cache_dir: directory in which the VEP cache should be downloaded
+    2) zip_name: name of the zip file to download
+    3) url: complete URL of the file to download
+    4) image: docker image on which to create a container with Docker or Singularity
+    5) filters: "--filter "
+    6) impact_levels: select the impact level, as a list of strings (ex. ["MODERATE", "HIGH"]
+    7) species: currently only needed to give a directory name