FEA: modifie snakefile variables for snakeckdysis integration

RNAja/snakefiles/Snakefile

@@ -159,7 +159,7 @@ rule run_Fastqc:
         error = f"{log_dir}/run_Fastqc/{{fastq}}.e",
         output = f"{log_dir}/run_Fastqc/{{fastq}}.o"
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
          """
          fastqc -o {out_dir}/1_QC/fastqc -t {threads} {input.fastq}
@@ -193,7 +193,7 @@ rule hisat2_index:
         error = f"{log_dir}/{name_hisat_index}_HISAT-INDEX.e",
         output = f"{log_dir}/{name_hisat_index}_HISAT-INDEX.o",
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         ln -s {input.reference} {output.index} 1>{log.output} 2>{log.error}
@@ -222,7 +222,7 @@ rule hisat2_map:
             bam: {output.bam}                                                                                                 
         """
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         hisat2 --dta -p {threads} -x {input.reference} -U {input.r1} --summary-file {output.summary} | samtools view -S -b > {output.bam} 
@@ -252,7 +252,7 @@ rule bam_sort:
             mapped_bam: {output.mapped_hisat}
         """
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         samtools sort  {input.hisat} > {output.out_hisat}
@@ -276,7 +276,7 @@ rule generate_bamfile_info:
     output:
         out_file = f"{out_dir}/2_mapping/bamfile_info.txt"
     script:
-        f"{RNAja.RNAJA_SCRIPTS}/write_bamfile_info.py"
+        f"{RNAja_obj.snakemake_scripts}/write_bamfile_info.py"
 
 
 rule samtools_stats:
@@ -308,7 +308,7 @@ rule samtools_stats:
                     - LOG output: {{log.output}}
             {sep*108}"""
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
             """
                 samtools stats {input.sorted_bam_file} > {input.sorted_bam_file}.bamStats.txt 2>>{log.error}
@@ -349,7 +349,7 @@ rule stringtie_discovery :
         Execute {rule}
         """
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         stringtie -p 8 -B -G {input.gtf} -o {output.hisat_gtf} -A {output.hisat_tsv} {input.bam_hisat}
@@ -380,7 +380,7 @@ rule merge_stringtie_gtf_discovery:
         Execute {rule}
         """
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         stringtie --merge -p 4 -G {input.gtf_ref} -o {output.gtf_merged} {input.list_gtf_hisat}
@@ -404,7 +404,7 @@ rule stringtie :
         Execute {rule}
         """
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         stringtie -p 8 -e -B -G {input.gtf} -o {output.hisat_gtf} -A {output.hisat_tsv} {input.bam_hisat}
@@ -436,7 +436,7 @@ rule merge_stringtie_gtf:
         Execute {rule}
         """
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         stringtie --merge -p 4 -G {input.gtf_ref} -o {output.gtf_merged} {input.list_gtf_hisat}
@@ -464,7 +464,7 @@ rule prepDE_stringtie_table:
         gcsv_hisat = f'{out_dir}/3_count/STRINGTIE/HISAT_gene_count_matrix.csv',
         tcsv_hisat = f'{out_dir}/3_count/STRINGTIE/HISAT_transcript_count_matrix.csv',
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     shell:
         """
         prepDE.py -i {input.mergelist_hisat} -t {output.tcsv_hisat} -g {output.gcsv_hisat}
@@ -496,6 +496,6 @@ rule diff_exp_analysis:
         error = f"{log_dir}/diff_exp_analysis.e",
         output = f"{log_dir}/diff_exp_analysis.o"
     singularity:
-        config["SINGULARITY"]["MAIN"]
+        tools_config["SINGULARITY"]["TOOLS"]
     script:
-        f"{RNAja.RNAJA_SCRIPTS}/EdgeR.R"
+        f"{RNAja_obj.snakemake_scripts}/EdgeR.R"