Debug {{

frangiPANe/snakefiles/fastq_stats.smk

@@ -8,13 +8,13 @@ rule fastq_stats:
         error = f"{frangipane_obj.path_logs}/stats/{{fastq_file}}.e"
     message:
          f"""--------------------
--Running {rule}
+-Running {{rule}}
 |-- Input:
-|   - Fastq dir : {frangipane_obj.path_fastq}
+|   - Fastq dir : {{frangipane_obj.path_fastq}}
 |-- Output:
-|   - Fastq stat dir: {frangipane_obj.path_stat_fastq}
+|   - Fastq stat dir: {{frangipane_obj.path_stat_fastq}}
 |-- Other infos:
-|   - LOG output : {log.output} 
+|   - LOG output : {{log.output}}
 --------------------
 """
     singularity:

frangiPANe/snakefiles/filter_length.smk

@@ -10,13 +10,13 @@ rule filter_length:
         length = frangipane_obj.get_config_value("CONTIGS","minLength")
     message:
         f"""--------------------
--Running {rule}
+-Running {{rule}}
 |-- Input:
-|   - fasta files: {frangipane_obj.path_contigs}
+|   - fasta files: {{frangipane_obj.path_contigs}}
 |-- Output:
-|   - fasta dir: {frangipane_obj.path_filtered_contigs}
+|   - fasta dir: {{frangipane_obj.path_filtered_contigs}}
 |-- Other infos:
-|   - LOG output : {log.output} 
+|   - LOG output : {{log.output}} 
 --------------------
 """
     run:

frangiPANe/snakefiles/merge_fastq_stats.smk

@@ -10,11 +10,11 @@ rule merge_fastq_stats:
             f"""--------------------
 -Running {{rule}}
 |-- Input:
-|   - Fastq stats : {frangipane_obj.path_stat_fastq}
+|   - Fastq stats : {{frangipane_obj.path_stat_fastq}}
 |-- Output:
-|   - stat file: {output.stat_file}
+|   - stat file: {{output.stat_file}}
 |-- Other infos:
-|   - LOG output : {log.output} 
+|   - LOG output : {{log.output}} 
 --------------------
 """
     run:

frangiPANe/snakefiles/merge_flagstat.smk

@@ -10,11 +10,11 @@ rule merge_flagstat:
          f"""--------------------
 -Running {{rule}}
 |-- Input:
-|   - Bam stat directory : f"{frangipane_obj.path_bam}"
+|   - Bam stat directory : {{frangipane_obj.path_bam}}
 |-- Output:
 |   - Stat file: {{output.stat_file}}
 |-- Other infos:
-|   - LOG output : {log.output} 
+|   - LOG output : {{log.output}}
 --------------------
 """
     run:

frangiPANe/snakefiles/plot_fasta.smk

@@ -11,12 +11,12 @@ rule plot_fasta:
          f"""--------------------
 -Running {{rule}}
 |-- Input:
-|    - Fasta : {input.ref}
+|    - Fasta : {{input.ref}}
 |-- Output:
-|    - Plot : {output.png}
-|    - Csv : {output.csv}
+|    - Plot : {{output.png}}
+|    - Csv : {{output.csv}}
 |-- Other infos:
-|    - LOG output : {log.output} 
+|    - LOG output : {{log.output}} 
 --------------------
 """
     run:

frangiPANe/snakefiles/plot_fastq.smk

@@ -18,11 +18,11 @@ rule plot_fastq:
          f"""--------------------
 -Running {{rule}}
 |-- Input:
-|    - Stat file : {input.csv}
+|    - Stat file : {{input.csv}}
 |-- Output:
-|    - Plot : {params.plot_dir}
+|    - Plot : {{params.plot_dir}}
 |-- Other infos:
-|    - LOG output : {log.output} 
+|    - LOG output : {{log.output}} 
 --------------------
 """
     run:

frangiPANe/snakefiles/plot_mapping.smk

@@ -11,11 +11,11 @@ rule plot_mapping:
          f"""--------------------
 -Running {{rule}}
 |-- Input:
-|    - Stat file : {input.csv}
+|    - Stat file : {{input.csv}}
 |-- Output:
-|    - Plot : {output.png_mapping}
+|    - Plot : {{output.png_mapping}}
 |-- Other infos:
-|    - LOG output : {log.output} 
+|    - LOG output : {{log.output}} 
 --------------------
 """
     run:

frangiPANe/snakefiles/samtools_view.smk

@@ -15,14 +15,14 @@ rule samtools_view:
         f"""--------------------
 -Running {{rule}}
 |-- Input:
-|   - bam file : {input.bam_file}
+|   - bam file : {{input.bam_file}}
 |-- Output:
-|   - bam file: {output.bam_file}
+|   - bam file: {{output.bam_file}}
 |-- Others infos :
-|   -Threads : {threads}
-|   -LOG output: {log.output}
-|   -LOG error: {log.error}
-|   -Other options: {params.other_options}
+|   -Threads : {{threads}}
+|   -LOG output: {{log.output}}
+|   -LOG error: {{log.error}}
+|   -Other options: {{params.other_options}}
 --------------------
 """
     singularity:

frangiPANe/snakefiles/vecscreen.smk

@@ -13,11 +13,11 @@ rule vecscreen:
         f"""--------------------
 -Running {{rule}}
 |-- Input:
-|   - fasta files: {input.fasta_file}
+|   - fasta files: {{input.fasta_file}}
 |-- Output:
-|   - fasta dir: {output.fasta_file}
+|   - fasta dir: {{output.fasta_file}}
 |-- Others infos :
-|   - Filtering on sequences longer than  : {params.length}
+|   - Filtering on sequences longer than  : {{params.length}}
 --------------------
 """
     run: