Adding log related to update with singu+load env

frangiPANe/snakefiles/filter_length.smk

@@ -3,9 +3,8 @@ rule filter_length:
         fasta_file = f"{frangipane_obj.path_contigs}/{{sample_name}}-{{ref_name}}/{{sample_name}}-{{ref_name}}-contigs.fa"
     output:
         fasta_file = f"{frangipane_obj.path_filtered_contigs}/{{sample_name}}-{{ref_name}}-contigs.fa"
-   #log:
-   #     error =  f"{log_dir}/abyss-filtered/{{sample_name}}-{{ref_name}}.log.e",
-   #     output = f"{log_dir}/abyss-filtered/{{sample_name}}-{{ref_name}}.log.o"
+    log:
+        output = f"{log_dir}/abyss-filtered/filtering.log.o"
     params:
         length = frangipane_obj.get_config_value("CONTIGS","minLength"),
         dirout = frangipane_obj.path_filtered_contigs

frangiPANe/snakefiles/plot_fasta.smk

@@ -5,6 +5,8 @@ rule plot_fasta:
     output: 
         png = f"{path_dico['plot']}/00_{ref_basename}.png",
         csv = f"{path_dico['sum']}/00_{ref_basename}.txt",
+    log:
+        output = f"{frangipane_obj.path_logs}/plot/plot_fasta.o"
     message:
          f"""--------------------
 -Running {{rule}}

frangiPANe/snakefiles/plot_fastq.smk

@@ -11,6 +11,8 @@ rule plot_fastq:
         png_base=Path(frangipane_obj.path_stat_plot,"sample_reads_base_ratio.png"),
     params:
         plot_dir = frangipane_obj.path_stat_plot
+    log:
+        output = f"{frangipane_obj.path_logs}/plot/plot_fastq.o",
     message:
          f"""--------------------
 -Running {{rule}}

frangiPANe/snakefiles/plot_mapping.smk

@@ -4,6 +4,9 @@ rule plot_mapping:
         group=f"{frangipane_obj.path_group}",
     output: 
         png_mapping=f"{frangipane_obj.path_stat_plot}/mapping_read_ratio-{frangipane_obj.reference_basename}.png",
+    log:
+        output = f"{frangipane_obj.path_logs}/plot/plot_mapping.o"
+
     message:
          f"""--------------------
 -Running {{rule}}