Merge branch 'master' into add_neovax_workflows

broadinstitute · May 10, 2024 · 490473e · 490473e
2 parents cc49361 + 4afbfdd
commit 490473e
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diff --git a/.dockstore.yml b/.dockstore.yml
@@ -128,4 +128,9 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /NeoVax/NeoVax_PackageData/NeoVax_PackageData.wdl
    testParameterFiles:
-    - /NeoVax/NeoVax_PackageData/NeoVax_PackageData.inputs.json
+    - /NeoVax/NeoVax_PackageData/NeoVax_PackageData.inputs.json
+ - name: QUICviz
+   subclass: WDL
+   primaryDescriptorPath: /PECGS-QUICviz/QUICviz.wdl
+   testParameterFiles:
+    - /PECGS-QUICviz/QUICviz.inputs.json
diff --git a/PECGS-QUICviz/QUICviz.inputs.json b/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"
+}
+
diff --git a/PECGS-QUICviz/QUICviz.wdl b/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: "[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
+        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"
+    }
+}
diff --git a/SmartSeq/SC_Plate_QC/SC_Plate_QC.wdl b/SmartSeq/SC_Plate_QC/SC_Plate_QC.wdl
@@ -219,7 +219,7 @@ task graphPlate{
 
 	runtime {
 	    docker: "bgranger/ss2_qc:0.1"
-        memory: memory + "GB"
+        memory: memory + " GB"
         cpu: "2"
 		disks: "local-disk "+disk_space+" HDD"
         bootDiskSizeGb: boot_disk_space

diff --git a/SmartSeq/scRNA_Pipeline/SmartSeq2_scRNA_pipeline.wdl b/SmartSeq/scRNA_Pipeline/SmartSeq2_scRNA_pipeline.wdl
@@ -172,7 +172,7 @@ task AdapterQC {
     runtime {
       docker: ss2_adapter_qc_docker
       disks: "local-disk " + disk_size + " HDD"
-      memory: mem + "GB"
+      memory: mem + " GB"
       cpu: "1"
     }
     output {
@@ -209,7 +209,7 @@ task ExtractQC_metrics {
     runtime {
       docker: ss2_docker
       disks: "local-disk 25 HDD"
-      memory: mem + "GB"
+      memory: mem + " GB"
       cpu: "1"
     }
 

diff --git a/SmartSeq/scRNA_Pipeline/SmartSeq_wdls/hisat2_rsem_descriptor.wdl b/SmartSeq/scRNA_Pipeline/SmartSeq_wdls/hisat2_rsem_descriptor.wdl
@@ -145,7 +145,7 @@ task HISAT2rsem {
   }
   runtime {
     docker:"quay.io/humancellatlas/secondary-analysis-hisat2:v0.2.2-2-2.1.0"
-    memory: Rsem_memory + "GB"
+    memory: Rsem_memory + " GB"
     disks: "local-disk " + disk_size + " HDD"
     cpu: "4"
     preemptible: 5
@@ -192,7 +192,7 @@ task RsemExpression {
   }
   runtime {
     docker: "quay.io/humancellatlas/secondary-analysis-rsem:v0.2.2-1.3.0"
-    memory: Rsem_exp_memory + "GB"
+    memory: Rsem_exp_memory + " GB"
     disks: "local-disk " + disk_size + " HDD"
     cpu: "4"
     preemptible: 5