Patch 1

TIL_pipeline/input_file.json

@@ -0,0 +1,7 @@
+[
+    {
+       "wf_quip_lymphocyte_segmentation.imageToBeProcessed": "gs://nuclear_seqmentation_quip_cnn_pipeline/input_images/TCGA_TEST.svs",
+       "wf_quip_lymphocyte_segmentation.resultName":"TCGA_TEST_rand",
+       "wf_quip_lymphocyte_segmentation.BORBcompatible":"true"
+    }
+]

TIL_pipeline/lymphocyte_job.wdl

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+task quip_lymphocyte_segmentation {
+  File originalInput
+  String result 
+  String? BORBcompatible
+  command {
+      echo "$(date): Till Segment has begun "
+      cd /root/quip_classification 
+      chmod a+x ./til_segment_process.sh 
+      time ./til_segment_process.sh -originalInput=${originalInput} -result="${result}".tar.gz -BORBcompatible=BORBcompatible
+      echo "$(date): Task: Til segment has finished"
+    }
+    output {
+      File out="${result}.tar.gz"
+    }
+    runtime {
+      docker: "us.gcr.io/cloudypipelines-com/til_segmentation:1.3"
+      bootDiskSizeGb: 70
+      disks: "local-disk 70 SSD"
+      memory:  "52 GB"
+      cpu: "8"
+      maxRetries: 1
+      gpuCount: 1
+      preemptible:3
+      zones: "us-east1-d us-east1-c us-central1-a us-central1-c us-west1-a us-west1-b"
+      gpuType: "nvidia-tesla-t4"
+      nvidiaDriverVersion: "418.40.04"
+    }
+ }
+workflow wf_quip_lymphocyte_segmentation{ 
+  File imageToBeProcessed
+  String resultName 
+  String? BORBcompatible
+  call quip_lymphocyte_segmentation {input: originalInput=imageToBeProcessed,result=resultName,BORBcompatible=BORBcompatible}
+  output {
+     quip_lymphocyte_segmentation.out
+  }
+} 

TIL_pipeline/quip_lymphocyte_segmentationWithConversion.wdl

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+task vsi_detector {
+  String fileInput
+  command {
+    is_vsi.sh ${fileInput}
+  }
+  output {
+    Boolean out=read_boolean(stdout())
+  }
+  runtime {
+    docker: "us.gcr.io/cloudypipelines-com/quip_vsi_detector:1.0"
+    memory:  "3.75 GB"
+    cpu: "1"
+    maxRetries: 1
+    zones: "us-east1-b us-east1-c us-east1-d us-central1-a us-central1-b us-central1-c us-central1-f us-east4-a us-east4-b us-east4-c us-west1-a us-west1-b us-west1-c us-west2-a us-west2-b us-west2-c"
+  }
+}
+
+task convert {
+  File vsiInput
+  String tifOutput
+  command {
+    echo "$(date): Task: convert started"
+    cd /root
+    time ./converter_process.sh ${vsiInput} "${tifOutput}.tif"
+    echo "$(date): Task: convert finished"
+  }
+  output {
+    File out="${tifOutput}.tif"
+  }
+  runtime {
+    docker: "us.gcr.io/cloudypipelines-com/quip_converter_to_tiff:1.1"
+    bootDiskSizeGb: 50
+    disks: "local-disk 50 SSD"
+    memory:  "12 GB"
+    cpu: "2"
+    maxRetries: 1
+    zones: "us-east1-b us-east1-c us-east1-d us-central1-a us-central1-b us-central1-c us-central1-f us-east4-a us-east4-b us-east4-c us-west1-a us-west1-b us-west1-c us-west2-a us-west2-b us-west2-c"
+  }
+}
+
+task quip_lymphocyte_segmentation {
+  File? imageInput  
+  File originalInput
+  String result 
+  String? BORBcompatible
+  command {
+      echo "$(date): Till Segment has begun "
+      cd /root/quip_classification 
+      chmod a+x ./til_segment_process.sh 
+      time ./til_segment_process.sh -originalInput=${originalInput} -imageInput=${imageInput} -result="${result}".tar.gz -BORBcompatible=BORBcompatible
+      echo "$(date): Task: Til segment has finished"
+    }
+    output {
+      File out="${result}.tar.gz"
+    }
+    runtime {
+      docker: "us.gcr.io/cloudypipelines-com/til_segmentation:1.3"
+      bootDiskSizeGb: 70
+      disks: "local-disk 70 SSD"
+      memory:  "52 GB"
+      cpu: "8"
+      maxRetries: 1
+      gpuCount: 1
+      zones: "us-east1-d us-east1-c us-central1-a us-central1-c us-west1-a us-west1-b"
+      gpuType: "nvidia-tesla-t4"
+      nvidiaDriverVersion: "418.40.04"
+    }
+ }
+
+
+workflow wf_quip_lymphocyte_segmentation{ 
+  File imageToBeProcessed
+  String resultName 
+  String? BORBcompatible
+  #Detect if input image is vsi or not 
+  call vsi_detector {input: fileInput=imageToBeProcessed} 
+  Boolean should_call_convert = vsi_detector.out 
+  if(should_call_convert){
+    call convert {input: vsiInput=imageToBeProcessed,tifOutput=resultName} 
+    File convert_out = convert.out
+  }#do standard process  
+  File? convert_out_maybe = convert_out
+  call quip_lymphocyte_segmentation {input: imageInput=convert_out_maybe,originalInput=imageToBeProcessed,result=resultName,BORBcompatible=BORBcompatible}
+  output {
+     quip_lymphocyte_segmentation.out
+  }
+}