fix errors

Snakefile

@@ -513,6 +513,8 @@ if config["bamCoverage"]["do"]:
     bamCoverage_options = config['bamCoverage']['options']
     if config["bamCoverage"]["spike-in"] and config["design"]["spike"]:
         bamCoverage_scaleFactor = compute_scaling_factor_output
+    else:
+        bamCoverage_scaleFactor = "{}/{{SAMPLE}}_{{REF}}_sort{}.bam".format(biasedRegions_dir, biasedRegions)
     final_output.extend(expand(bamCoverage_output,  SAMPLE=samples, REF=ref, allow_missing=True))    
     include: os.path.join(RULES, "bamCoverage.rules")  
 

config/config.yaml

@@ -287,7 +287,7 @@ differential_analysis:
 bamCoverage:
     do: yes
     options: "--binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC" 
-    spike-in: yes
+    spike-in: no
     threads: 4
 
 #############################################################################

workflow/rules/bamCoverage.rules

@@ -24,7 +24,8 @@
 
 rule bamCoverage:
     input:
-        bamCoverage_input
+        bam = bamCoverage_input,
+        scaleFactor = bamCoverage_scaleFactor
     log:
         out = bamCoverage_logs
     output:
@@ -32,20 +33,19 @@ rule bamCoverage:
     singularity:
         "epeak.img"
     params:
-        options = bamCoverage_options,
-        scaleFactor = bamCoverage_scaleFactor
+        options = bamCoverage_options
     envmodules:
         "deepTools"
     threads:
         config['bamCoverage']['threads']
     shell:
         """
-        if [[ -s {params.scaleFactor} && {params.scaleFactor} == *"_scaleFactor.txt"*  ]]
+        if [[ -s {input.scaleFactor} && {input.scaleFactor} == *"_scaleFactor.txt"*  ]]
         then
-            S=$(cat {params.scaleFactor})
-            bamCoverage --bam {input} --outFileName {output} {params.options} --scaleFactor $S --numberOfProcessors {threads} 2> {log.out}
+            S=$(cat {input.scaleFactor})
+            bamCoverage --bam {input.bam} --outFileName {output} {params.options} --scaleFactor $S --numberOfProcessors {threads} 2> {log.out}
         else 
-            bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log.out}
+            bamCoverage --bam {input.bam} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log.out}
         fi
         
         """

workflow/rules/bedgraph.rules

@@ -44,7 +44,6 @@ rule bedgraph:
         if [[ -s {input.scaleFactor} && {input.scaleFactor} == *"_scaleFactor.txt"*  ]]
         then
             S=$(cat {input.scaleFactor})
-            echo $S
             bedtools genomecov -bg -i $temp_file -g {params.genome} -scale $S > {output} 2> {log.out}
         else 
             bedtools genomecov -bg -i $temp_file -g {params.genome} > {output} 2> {log.out}