fasta plot

frangiPANe/snakefiles/common.smk

@@ -62,15 +62,15 @@ def get_output_final(wildcards):
         dico_output.update({
                 "merge_fastq_stats" : rules.merge_fastq_stats.output })
 
-        if not "panref" in REF:
-            dico_output.update({
-                "plot_fastq" : expand(rules.plot_fastq.output, ref_name=REF)})
+        dico_output.update({
+                "plot_fastq" : rules.plot_fastq.output})
 
             # STAT ASSEMBLY
         dico_output.update({
                 "fasta_stats2" : rules.fasta_stats2.output}),
 
-        dico_output.update({
+        if not "panref" in REF:
+            dico_output.update({
                 "fasta_stats" : rules.fasta_stats.output}),
 
             # STAT MAPPING

frangiPANe/snakefiles/generate_jupyter_book.smk

 rule generate_jupyter_book:
     input:
         jb_file=f"{ frangipane_obj.install_path }/report/frangiPANe_report.ipynb",
-        ref_png=rules.plot_fasta.output.png,
-        ref_csv=rules.plot_fasta.output.csv
+        ref_png=f"{frangipane_obj.path_stat_plot}/00_ref.png",
+        ref_csv = f"{frangipane_obj.path_stat_sum}/00_ref.txt"
     output:
         jb_file=f"{ frangipane_obj.path_output }/report/frangiPANe_stats.ipynb"
     log:

frangiPANe/snakefiles/plot_fasta.smk

@@ -2,11 +2,11 @@ rule plot_fasta:
     input:
         ref=rules.bwa_index.input.ref
     output: 
-        png = f"{frangipane_obj.path_stat_plot}/00_{{ref_name}}.png",
-        csv = f"{frangipane_obj.path_stat_sum}/00_{{ref_name}}.txt"
+        png = f"{frangipane_obj.path_stat_plot}/00_ref.png",
+        csv = f"{frangipane_obj.path_stat_sum}/00_ref.txt"
     log:
-        output = f"{frangipane_obj.path_logs}/report/plot_{{ref_name}}.o",
-        error = f"{frangipane_obj.path_logs}/report/plot_{{ref_name}}.e"
+        output = f"{frangipane_obj.path_logs}/report/plot_ref.o",
+        error = f"{frangipane_obj.path_logs}/report/plot_ref.e"
     message:
          f"""--------------------
 -Running {{rule}}