add rulegraph - add spike-in in bamcoverage - add do to dedup

config/config.yaml

@@ -271,20 +271,23 @@ differential_analysis:
     input_counting: no
 
 
+
 #############################################################################
 # bamCoverage from Deeptools
 #  see https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
 #
 # :Parameters:
 #
-# - do: if 'no', this rule is ignored.
-# - options: any parameter recognized by Deeptools (see Deeptools manual)
-#
-#===============================================================================
+# - do: if unchecked, this rule is ignored
+# - options: options related to deeptools
+# - spike-in: set to yes to use spike-in data as sacaling factor
+# see https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
+# for more information about effective Genome Size
 
 bamCoverage:
     do: yes
     options: "--binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC" 
+    spike-in: yes
     threads: 4
 
 #############################################################################

workflow/rules/bamCoverage.rules

@@ -32,12 +32,20 @@ rule bamCoverage:
     singularity:
         "epeak.img"
     params:
-        options = bamCoverage_options
+        options = bamCoverage_options,
+        scaleFactor = bamCoverage_scaleFactor
     envmodules:
         "deepTools"
     threads:
         config['bamCoverage']['threads']
     shell:
         """
-        bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log.out}
+        if [[ -s {params.scaleFactor} && {params.scaleFactor} == *"_scaleFactor.txt"*  ]]
+        then
+            S=$(cat {params.scaleFactor})
+            bamCoverage --bam {input} --outFileName {output} {params.options} --scaleFactor $S --numberOfProcessors {threads} 2> {log.out}
+        else 
+            bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log.out}
+        fi
+        
         """