added macs2 to CUTnRUN pipeline

CWL/tools/macs2_callpeak.cwl

@@ -0,0 +1,72 @@
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+hints:
+  ResourceRequirement:
+    coresMin: 1
+    ramMin: 10000
+  DockerRequirement:
+    dockerPull: genomicpariscentre/macs2:2.1.0.20140616
+
+### BASE COMMAND AND ARGUMENTS:
+##################################################
+baseCommand: ["macs2", "callpeak"]
+arguments:  
+  - valueFrom: |
+      ${
+        if ( inputs.is_paired_end ){
+           return "BAMPE";
+        }
+        else {
+          return "BAM";
+        }
+      }
+    prefix: --format
+    position: 1
+  - valueFrom: "--nomodel"
+    position: 2
+  - valueFrom: "all"
+    prefix: "--keep-dup"
+    position: 2
+  - valueFrom: $(inputs.bam.nameroot + ".macs2")
+    prefix: "--name"
+    position: 100
+
+inputs:
+  bam:
+    type: File
+    inputBinding:
+        position: 101
+        prefix: "--treatment"
+  genome_size:
+    type: long
+    inputBinding:
+        position: 3
+        prefix: "--gsize"
+  broad:
+    type: boolean
+    inputBinding:
+        position: 3
+        prefix: "--broad"
+  qvalue:
+    type: float
+    inputBinding:
+        position: 3
+        prefix: "--qvalue"
+  is_paired_end:
+    type: boolean
+    default: true
+
+outputs:
+  peaks_bed:    
+    type: 
+      type: array
+      items: File
+    outputBinding:
+      glob: "*Peak"
+  peaks_xls:
+    type: File
+    outputBinding:
+      glob: "*_peaks.xls"

CWL/workflows/CUTnRUN.cwl

@@ -123,6 +123,17 @@ inputs:
       Default: "chrX chrY chrM"
     type: string?
     default: "chrX chrY chrM"
+  macs2_qvalue:
+    doc: |
+      Q-value cutoff used for peak calling by MACS2. 
+      The default is 0.05.
+    type: float
+  broad_peaks:
+    doc: |
+      Determines whether the "--broad" flag
+      should be used by MACS2 for peak calling.
+    type: boolean
+    default: false
 
 ### WORKFLOW STEPS:
 ##################################################
@@ -230,6 +241,22 @@ steps:
     out:
       - bigwig
 
+  peak_calling_macs2:
+    doc: peak calling using macs2
+    run: "../tools/macs2_callpeak.cwl"
+    in:
+      bam:
+        source: merge_filter/bam
+      genome_size:
+        source: effective_genome_size
+      broad: 
+        source: broad_peaks
+      qvalue:
+        source: macs2_qvalue
+    out: 
+      - peaks_bed
+      - peaks_xls
+
   create_summary_qc_report:
     doc: |
       multiqc summarizes the qc results from fastqc 
@@ -358,6 +385,15 @@ outputs:
   qc_phantompeakqualtools_stderr:
     type: File?
     outputSource: chip_qc/qc_phantompeakqualtools_stderr
+
+  peaks_bed_macs2:
+    type:
+      type: array
+      items: File
+    outputSource: peak_calling_macs2/peaks_bed
+  peaks_xls_macs2:
+    type: File
+    outputSource: peak_calling_macs2/peaks_xls
 
   multiqc_zip:
     type: File