integrating group stats

frangiPANe/snakefiles/generate_jupyter_book.smk

@@ -5,6 +5,8 @@ rule generate_jupyter_book:
         ref_csv = f"{frangipane_obj.path_stat_sum}/00_ref.txt"
     output:
         jb_file=f"{ frangipane_obj.path_output }/report/frangiPANe_stats.ipynb"
+    params:
+        group_file = f"{frangipane_obj.path_group}"
     log:
         output = f"{frangipane_obj.path_logs}/report/jupyterBook.o",
         error = f"{frangipane_obj.path_logs}/report/jupyterBook.e"

frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py

@@ -12,7 +12,7 @@ jb_output = snakemake.output.jb_file
 
 # TODO26/11 : use class snakecdysis
 dico = {
-    "group_file": frangipane_obj.path_group,
+    "group_file": snakemake.params.group_file,
     "ref_file": frangipane_obj.path_reference_dir,
     "out_dir": frangipane_obj.path_output,
     "ref_png" : snakemake.input.ref_png,