update

Author: Nuwah12

wdl_tasks/peak_calling.wdl

@@ -60,8 +60,6 @@ task MACS2_CallPeaks {
 
     # Fragment size handling
     Int? estimated_fragment_size
-    Int default_extsize = 200
-    Int shift = 0
 
     # Runtime
     Int cpu = 4
@@ -88,7 +86,7 @@ task MACS2_CallPeaks {
       ~{if call_summits then "--call-summits" else ""} \
       ~{broad_flag} \
       ~{if defined(estimated_fragment_size) then "--nomodel" else ""} \
-      ~{if defined(HALF_FRAG) then ("--shiftsize="+HALF_FRAG) else ""} \
+      ~{if defined(estimated_fragment_size) then ("--shiftsize="+HALF_FRAG) else ""} \
       ~{if defined(estimated_fragment_size) then ("--bw="+Bandwidth) else ""} \
       ~{if paired_end then "--format BAMPE" else "--format BAM"} \
       --keep-dup=1 \

workflows/peak_calling/peakcalling.wdl

@@ -36,47 +36,33 @@ workflow MACS2_CallPeaks {
     	String bam = sample[1]     
 
 	if (HomerFragmentSizeEstimation) {
-		call peakcall.EstimateFragSize {
+		call peakcall.EstimateFragSize as FragmentSizeEstimator {
 			input:
 				bam = bam,
 				sample_name = sample_id
 		}
-	
-
-        	call peakcall.MACS2_CallPeaks {
-            		input:
-				treatment_bam = bam,
-				sample_name = sample_id,
-				control_bam = control_bam,
-				genome_size = genome_size,
-				q_value = q_value,
-				call_summits = call_summits,
-				paired_end = paired_end,
-				peak_type = peak_type,
-				cpu = cpu,
-				mem = mem
-        	}	
     	}
-	if (!HomerFragmentSizeEstimation) {
-		call peakcall.MACS2_CallPeaks {
-			input:
-				treatment_bam = bam,
-				sample_name = sample_id,
-				control_bam = control_bam,
-				genome_size = genome_size,
-				q_value = q_value,
-				call_summits = call_summits,
-				paired_end = paired_end,
-				peak_type = peak_type,
-				cpu = cpu,
-				mem = mem
-		}
+	
+	call peakcall.MACS2_CallPeaks as PeakCaller {
+		input:
+			treatment_bam = bam,
+			sample_name = sample_id,
+			control_bam = control_bam,
+			genome_size = genome_size,
+			q_value = q_value,
+			estimated_fragment_size = FragmentSizeEstimator.estimated_fragment_size,
+			call_summits = call_summits,
+			paired_end = paired_end,
+			peak_type = peak_type,
+			cpu = cpu,
+			mem = mem
 	}
-
     }
+
+   
     output {
-        Array[File] narrowPeak = MACS2_CallPeaks.narrowPeak
-        Array[File?] summits = MACS2_CallPeaks.summits
-        Array[File] xls = MACS2_CallPeaks.xls
+        Array[File] narrowPeak = PeakCaller.narrowPeak
+        Array[File?] summits = PeakCaller.summits
+        Array[File] xls = PeakCaller.xls
     }
 }