first commit of QUICviz WDL

.dockstore.yml

@@ -118,4 +118,9 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /CleanupFailedSubmissions/Cleanup_Failed_Submissions.wdl
    testParameterFiles:
-    - /CleanupFailedSubmissions/Cleanup_Failed_Submissions.inputs.json
+    - /CleanupFailedSubmissions/Cleanup_Failed_Submissions.inputs.json
+ - name: QUICviz
+   subclass: WDL
+   primaryDescriptorPath: /PECGS-QUICviz/QUICviz.wdl
+   testParameterFiles:
+    - /PECGS-QUICviz/QUICviz.inputs.json

PECGS-QUICviz/QUICviz.inputs.json

@@ -0,0 +1,11 @@
+{
+  "QUICviz.calledCopyRatioSegTumor": "File",
+  "QUICviz.oncotatedCalledTumor": "File",
+  "QUICviz.allelicCountsNormal": "File",
+  "QUICviz.denoisedCopyRatiosTumor": "File",
+  "QUICviz.denoisedCopyRatiosNormal": "File",
+  "QUICviz.allelicCountsTumor": "File",
+  "QUICviz.tumorType": "String",
+  "QUICviz.sampleID": "String"
+}
+

PECGS-QUICviz/QUICviz.wdl

@@ -0,0 +1,104 @@
+version 1.0
+
+workflow QUICviz {
+    input {
+        String sampleID
+        String tumorType
+        File allelicCountsNormal
+        File allelicCountsTumor
+        File denoisedCopyRatiosNormal
+        File denoisedCopyRatiosTumor
+        File calledCopyRatioSegTumor
+        File oncotatedCalledTumor
+    }
+    call QUICviz {
+        input:
+            sampleID = sampleID,
+            tumorType = tumorType,
+            allelicCountsNormal = allelicCountsNormal,
+            allelicCountsTumor = allelicCountsTumor,
+            denoisedCopyRatiosNormal = denoisedCopyRatiosNormal,
+            denoisedCopyRatiosTumor = denoisedCopyRatiosTumor,
+            calledCopyRatioSegTumor = calledCopyRatioSegTumor,
+            oncotatedCalledTumor = oncotatedCalledTumor
+    }
+    call mergeImages {
+        input:
+            SampleID = sampleID,
+            TumorType = tumorType,
+            plot = QUICviz.plot
+    }
+    output {
+        File QUICvizPDF = mergeImages.compiled_pdf
+    }
+    meta {
+        author: "Yueyao Gao"
+        email: "[email protected]"
+        description: "QUICviz.wdl is based on the QUICviz_v0.3 R script developed by Alex Neil, which is a tool for visualizing CNV data"
+    }
+}
+
+task QUICviz {
+    input {
+        String sampleID
+        String tumorType
+        File allelicCountsNormal
+        File allelicCountsTumor
+        File denoisedCopyRatiosNormal
+        File denoisedCopyRatiosTumor
+        File calledCopyRatioSegTumor
+        File oncotatedCalledTumor
+    }
+    command <<<
+        Rscript /BaseImage/CMI_QUICviz/scripts/QUICviz_v0.3.R \
+            --sample ~{sampleID} \
+            --tumor_type ~{tumorType} \
+            --normal_acf ~{allelicCountsNormal} \
+            --normal_cr ~{denoisedCopyRatiosNormal} \
+            --tumor_acf ~{allelicCountsTumor} \
+            --tumor_cr ~{denoisedCopyRatiosTumor} \
+            --tumor_cr_seg ~{calledCopyRatioSegTumor} \
+            --tumor_seg_oncotated ~{oncotatedCalledTumor} \
+            --output_dir /BaseImage/CMI_QUICviz/outputs/
+
+    >>>
+    output {
+        Array[File] plot = glob("/BaseImage/CMI_QUICviz/outputs/*.png")
+    }
+    runtime {
+        docker: "us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/cmi_quicviz:0.3.0"
+        memory: "16 GB"
+        cpu: "4"
+        disks: "local-disk 100 HDD"
+    }
+}
+task mergeImages {
+    input {
+        String SampleID
+        String TumorType
+        Array[File] plot
+    }
+    command <<<
+        for i in ~{plot}; do mv $i /output/images/; done
+
+        python <<CODE
+        pip3 install img2pdf
+        import img2pdf
+        import glob
+        import os
+
+        with open(f"/output/~{SampleID}_~{TumorType}_QUICviz.pdf","wb") as f:
+            f.write(img2pdf.convert(glob.glob("/output/images/*.jpg")))
+
+        CODE
+    >>>
+    output {
+        File compiled_pdf = "/output/~{SampleID}_~{TumorType}_QUICviz.pdf"
+    }
+    runtime {
+        docker: "us.gcr.io/tag-team-160914/neovax-parsley:2.2.1.0"
+        memory: "16 GB"
+        cpu: "4"
+        disks: "local-disk 100 HDD"
+    }
+}