Quicviz v0.4.2 WDL Update

PECGS-QUICviz/QUICviz.wdl

@@ -3,8 +3,9 @@ version 1.0
 workflow QUICviz {
     input {
         String sampleID
+        Boolean isPECGS = true
         String tumorType
-        String quicvizDocker = "us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/cmi_quicviz:0.3.1"
+        String quicvizDocker = "us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/cmi_quicviz:0.4.2"
         File allelicCountsNormal
         File allelicCountsTumor
         File denoisedCopyRatiosNormal
@@ -24,29 +25,23 @@ workflow QUICviz {
             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
+        File QUICvizPDF = QUICviz.QUICvizPDF
+        File GeneLevelCNV = QUICviz.GeneLevelCNV
+        File AllChrPlot = QUICviz.AllChrPlot
     }
+
     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"
+        description: "QUICviz.wdl is based on the QUICviz_v0.4 R script developed by Alex Neil, which is a tool for visualizing CNV data"
     }
 }
 
 task QUICviz {
     input {
         String sampleID
+        Boolean isPECGS
         String tumorType
         String quicvizDocker
         File allelicCountsNormal
@@ -57,13 +52,24 @@ task QUICviz {
         File oncotatedCalledTumor
         Int memory = 16
         Int cpu = 4
+        Int maxRetries = 3
     }
     command <<<
         set -e
         mkdir outputs
 
-        Rscript /BaseImage/CMI_QUICviz/scripts/CMI_QUICviz_v0.3.R \
-            --sample ~{sampleID} \
+        if ~{isPECGS}; then
+            IFS='-' read -r tumor_sample normal_sample <<< "~{sampleID}"
+            echo "Input Tumor Sample: $tumor_sample"
+            echo "Input Normal Sample: $normal_sample"
+        else
+            tumor_sample=~{sampleID}
+            echo "Input Tumor Sample: $tumor_sample"
+        fi
+
+
+        Rscript /BaseImage/CMI_QUICviz/scripts/CMI_QUICviz_v0.4.2.R \
+            --sample $tumor_sample \
             --tumor_type ~{tumorType} \
             --normal_acf ~{allelicCountsNormal} \
             --normal_cr ~{denoisedCopyRatiosNormal} \
@@ -73,52 +79,21 @@ task QUICviz {
             --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
+        mv outputs/*chromosome_plots.pdf outputs/~{sampleID}_chromosome_plots.pdf
+        mv outputs/*gene_level_calls.csv outputs/~{sampleID}_gene_level_calls.csv
+        mv outputs/*_all_chr.png outputs/~{sampleID}_All_chr.png
 
-        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"
+        File QUICvizPDF = "outputs/~{sampleID}_chromosome_plots.pdf"
+        File GeneLevelCNV = "outputs/~{sampleID}_gene_level_calls.csv"
+        File AllChrPlot = "outputs/~{sampleID}_All_chr.png"
     }
     runtime {
         docker: quicvizDocker
         memory: memory + " GB"
         cpu: cpu
         disks: "local-disk 100 HDD"
+        maxRetries: maxRetries
     }
-}
+}