Adjusted bamCoverage rule for deepTools version >=3. For older deepTool...

Adjusted bamCoverage rule for deepTools version >=3. For older deepTool versions, it will not work anymore.

example/input/config.json

@@ -68,7 +68,7 @@
   },
   "par_deepTools": {
     "effectiveGenomeSize": 2750000000,
-    "bamCoverage_normalizationCoverage": "normalizeTo1x",
+    "bamCoverage_normalizationCoverage": "RPGC",
     "bamCoverage_binSize": 10,
     "bamCoverage_otherOptions": "--extendReads --centerReads"
   }

src/Snakemake/Snakefile

@@ -323,12 +323,10 @@ for fileCur in inputFiles:
 
 #### Parameter for bamCoverage
 
+# This works for deepTools >= 3 only due to changes in argument names, versions < 3 fail here. deepTools must be updated then
 bamCoverage_normOption = config["par_deepTools"]["bamCoverage_normalizationCoverage"]
-if not (bamCoverage_normOption == "normalizeTo1x") and not (bamCoverage_normOption == "normalizeUsingRPKM") and not (bamCoverage_normOption == "ignoreForNormalization"):
-    raise AssertionError("The config parameter config[\"par_deepTools\"][\"bamCoverage_normalizationCoverage\"] has to be one of: normalizeTo1x, normalizeUsingRPKM, ignoreForNormalization")
-
-if bamCoverage_normOption == "normalizeTo1x":
-    bamCoverage_normOption = bamCoverage_normOption + " " + str(config["par_deepTools"]["effectiveGenomeSize"])
+if not (bamCoverage_normOption == "RPKM") and not (bamCoverage_normOption == "CPM") and not (bamCoverage_normOption == "BPM") and not (bamCoverage_normOption == "RPGC"):
+    raise AssertionError("The config parameter config[\"par_deepTools\"][\"bamCoverage_normalizationCoverage\"] has to be one of: RPKM, CPM, BPM, RPGC. Make sure you use deepTools version >=3")
 
 
 ###########################################################################
@@ -1762,6 +1760,7 @@ rule bamCoverage:
     benchmark: LOG_BENCHMARK_dir +  "/bamCoverage.{basename}.benchmark"
     conda: "condaEnvironments/deepTools.yaml"
     params:
+        genomeSize          = str(config["par_deepTools"]["effectiveGenomeSize"]),
         normalization       = bamCoverage_normOption,
         binSize             = config["par_deepTools"]["bamCoverage_binSize"],
         ignoreChr           = "chrX chrM",
@@ -1773,7 +1772,8 @@ rule bamCoverage:
                 bamCoverage \
                     --bam {input.bam} \
                     --binSize {params.binSize} \
-                    --{params.normalization} \
+                    --effectiveGenomeSize {params.genomeSize} \
+                    --normalizeUsing {params.normalization} \
                     {params.otherOptions} \
                     --numberOfProcessors {threads} \
                     --ignoreForNormalization {params.ignoreChr} \
@@ -1783,7 +1783,8 @@ rule bamCoverage:
                 bamCoverage \
                     --bam {input.bam} \
                     --binSize {params.binSize} \
-                    --{params.normalization} \
+                    --effectiveGenomeSize {params.genomeSize} \
+                    --normalizeUsing {params.normalization} \
                     {params.otherOptions} \
                     --numberOfProcessors {threads} \
                     --ignoreForNormalization {params.ignoreChr} \