integrating fasta plot

frangiPANe/snakefiles/generate_jupyter_book.smk

@@ -6,13 +6,8 @@ rule generate_jupyter_book:
     output:
         jb_file=f"{ frangipane_obj.path_output }/report/frangiPANe_stats.ipynb"
     log:
-        output = f"{frangipane_obj.path_logs}/report/log.o",
-        error = f"{frangipane_obj.path_logs}/report/log.e"
-    params:
-        out_dir= frangipane_obj.path_output,
-        fastq_dir=frangipane_obj.path_fastq,
-        group_file=frangipane_obj.path_group,
-        ref_file=frangipane_obj.path_reference_file,
-        vec_file=frangipane_obj.path_univec,
+        output = f"{frangipane_obj.path_logs}/report/jupyterBook.o",
+        error = f"{frangipane_obj.path_logs}/report/jupyterBook.e"
+
     script:
         f"{ frangipane_obj.snakemake_scripts }/generate_jb_frangiPANe.py"

frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py

@@ -12,13 +12,13 @@ jb_output = snakemake.output.jb_file
 
 # TODO26/11 : use class snakecdysis
 dico = {
-    "out_dir" : snakemake.params.out_dir,
-    "fastq_dir" : snakemake.params.fastq_dir,
-    "group_file" : snakemake.params.group_file,
-    "ref_file" : snakemake.params.ref_file,
-    "vec_file" : snakemake.params.vec_file,
-    "ref_png" : snakemake.input.png,
-    "ref_csv" : snakemake.input.csv
+    "ref_png" : snakemake.input.ref_png,
+    "ref_csv" : snakemake.input.ref_csv
+    #"out_dir": snakemake.params.out_dir,
+    #"fastq_dir": snakemake.params.fastq_dir,
+    #"group_file": snakemake.params.group_file,
+    #"ref_file": snakemake.params.ref_file,
+    #"vec_file": snakemake.params.vec_file,
 }
 
 with open(jb_input, "r", encoding="utf-8") as notebook_file: