Merge branch 'master' into tag-mop-yg

.dockstore.yml

@@ -123,4 +123,9 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /TAG_Mop/TAG_Mop.wdl
    testParameterFiles:
-    - /TAG_Mop/TAG_Mop.inputs.json
+    - /TAG_Mop/TAG_Mop.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 +1,124 @@
+version 1.0
+
+workflow QUICviz {
+    input {
+        String sampleID
+        String tumorType
+        String quicvizDocker = "us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/cmi_quicviz:0.3.1"
+        File allelicCountsNormal
+        File allelicCountsTumor
+        File denoisedCopyRatiosNormal
+        File denoisedCopyRatiosTumor
+        File calledCopyRatioSegTumor
+        File oncotatedCalledTumor
+    }
+    call QUICviz {
+        input:
+            sampleID = sampleID,
+            tumorType = tumorType,
+            quicvizDocker = quicvizDocker,
+            allelicCountsNormal = allelicCountsNormal,
+            allelicCountsTumor = allelicCountsTumor,
+            denoisedCopyRatiosNormal = denoisedCopyRatiosNormal,
+            denoisedCopyRatiosTumor = denoisedCopyRatiosTumor,
+            calledCopyRatioSegTumor = calledCopyRatioSegTumor,
+            oncotatedCalledTumor = oncotatedCalledTumor
+    }
+
+    Array[File] QUICvizPlots = QUICviz.plot
+    call mergeImages {
+        input:
+            SampleID = sampleID,
+            TumorType = tumorType,
+            plot = QUICvizPlots,
+            quicvizDocker = quicvizDocker
+    }
+    output {
+        File QUICvizPDF = mergeImages.chr_pdf
+        File AllChrPlot = mergeImages.allchr_plot
+    }
+    meta {
+        author: "Yueyao Gao"
+        email: "tag@broadinstitute.org"
+        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
+        String quicvizDocker
+        File allelicCountsNormal
+        File allelicCountsTumor
+        File denoisedCopyRatiosNormal
+        File denoisedCopyRatiosTumor
+        File calledCopyRatioSegTumor
+        File oncotatedCalledTumor
+        Int memory = 16
+        Int cpu = 4
+    }
+    command <<<
+        set -e
+        mkdir outputs
+
+        Rscript /BaseImage/CMI_QUICviz/scripts/CMI_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 outputs/
+
+    >>>
+    output {
+        Array[File] plot = glob("outputs/*.png")
+    }
+    runtime {
+        docker: quicvizDocker
+        memory: memory + " GB"
+        cpu: cpu
+        disks: "local-disk 100 HDD"
+    }
+}
+task mergeImages {
+    input {
+        String SampleID
+        String TumorType
+        Array[File] plot
+        String quicvizDocker
+        Int memory = 16
+        Int cpu = 4
+    }
+    command <<<
+        mkdir -p output/images
+        for i in `ls ~{sep=" " plot}`; do mv $i output/images/; done
+
+        python3 <<CODE
+        import img2pdf
+        import glob
+        import os
+
+        # Get list of PNG files sorted
+        png_files = sorted(glob.glob("output/images/*.png"))
+        numeric_png_files = [file for file in png_files if os.path.basename(file).split('.')[0].isdigit()]
+        png_files = sorted(numeric_png_files, key=lambda x: int(os.path.basename(x).split('.')[0]))
+
+        with open(f"output/~{SampleID}_~{TumorType}_QUICviz.pdf","wb") as f:
+            f.write(img2pdf.convert(png_files))
+        CODE
+    >>>
+    output {
+        File chr_pdf = "output/~{SampleID}_~{TumorType}_QUICviz.pdf"
+        File allchr_plot = "output/images/All_chr.png"
+    }
+    runtime {
+        docker: quicvizDocker
+        memory: memory + " GB"
+        cpu: cpu
+        disks: "local-disk 100 HDD"
+    }
+}