Update Snakefile

Snakefile

@@ -22,6 +22,7 @@
 #########################################################################
 
 
+
 import pandas as pd
 from fnmatch import fnmatch
 from re import sub, match
@@ -40,9 +41,6 @@ RULES = os.path.join("workflow", "rules")
 # list of all files in the directory 'input_dir'
 
 filenames = [f for f in os.listdir(config["input_dir"]) if match(r'.*'+config["input_readtag"]+config["input_extension"]+'', f)] 
-samples = [sub(config["input_readtag"]+config["input_extension"], '', file) for file in filenames]
-receptor = [ x.strip() for x in (config["design"]["receptor"]).split(",")]
-conds = [ x.strip() for x in (config["design"]["condition"]).split(",")]
 
 
 #-------------------------------------------------------
@@ -118,9 +116,6 @@ else:
     __adapters__output = __input_data
     
     
-    
-    
-    
 ## Indexing genome
 ref = [ config["genome"]["name"] ]
 
@@ -165,33 +160,6 @@ expected_output.extend(expand(__bowtie2_mapping__sort, SAMPLE=samples, REF=ref))
 include: os.path.join(RULES, "bowtie2_mapping.rules")
       
     
-# then we performed peak calling only in files against reference genome and not spike genome !
-ref = config["genome"]["name"] 
-   
-# Genome coverage for plus and minus strand
-strand = ["minus", "plus"]
-__genomecov__input = "02-Mapping/{{SAMPLE}}_{}_sort.bam".format(ref)
-__genomecov__logs = "03-Coverage/logs/{SAMPLE}_{STRAND}_coverage.out"
-__genomecov__output = "03-Coverage/{SAMPLE}_{STRAND}_coverage.csv"
-__genomecov__genome = config["genome"]["fasta_file"]
-__genomecov__options = "" 
-
-expected_output.extend(expand(__genomecov__output, SAMPLE=samples, STRAND=strand))
-include: os.path.join(RULES, "genomecov.rules")
-
-
-
-# RNAsig R script
-__rnasig__target = "config/design_strand.txt"
-__rnasig__output_dir = "."
-__rnasig__covdir = "03-Coverage/"
-__rnasig__gfffile = config['genome']['gff_file']
-__rnasig__report = "04-RNAsig/finalplot.pdf"
-__rnasig__logs_out = "04-RNAsig/logs/rnasig.out"
-__rnasig__logs_err = "04-RNAsig/logs/rnasig.err"
-
-expected_output.extend([__rnasig__report])
-include: os.path.join(RULES, "rnasig.rules")
 
 # Multiqc rule
 config['multiqc']['options'] += " -c config/multiqc_config.yaml" 
@@ -206,7 +174,7 @@ expected_output = [__multiqc__output]
 include: os.path.join(RULES, "multiqc.rules")
 
 
-rule rnasig:
+rule rnaflow:
     input: expected_output