Update cellbender_remove_background.wdl

wdl/cellbender_remove_background.wdl

@@ -1,4 +1,4 @@
-## Copyright Broad Institute, 2019
+## Copyright Broad Institute, 2020
 ##
 ## LICENSING :
 ## This script is released under the WDL source code license (BSD-3)
@@ -10,6 +10,9 @@ task run_cellbender_remove_background_gpu {
   String sample_name
   File input_10x_h5_file_or_mtx_directory
 
+  # Outputs
+  String output_directory  # Google bucket path
+
   # Docker image for cellbender remove-background version
   String? docker_image = "us.gcr.io/broad-dsde-methods/cellbender:latest"
 
@@ -18,19 +21,21 @@ task run_cellbender_remove_background_gpu {
   Int? total_droplets_included
   String? model
   Int? low_count_threshold
+  String? fpr  # in quotes: floats separated by whitespace: the output false positive rate(s)
   Int? epochs
   Int? z_dim
   String? z_layers  # in quotes: integers separated by whitespace
-  String? d_layers  # in quotes: integers separated by whitespace
-  String? p_layers  # in quotes: integers separated by whitespace
   Float? empty_drop_training_fraction
   String? blacklist_genes  # in quotes: integers separated by whitespace
   Float? learning_rate
 
   # Hardware-related inputs
   String? hardware_zones = "us-east1-d us-east1-c us-central1-a us-central1-c us-west1-b"
   Int? hardware_disk_size_GB = 50
+  Int? hardware_boot_disk_size_GB = 20
   Int? hardware_preemptible_tries = 2
+  Int? hardware_cpu_count = 4
+  Int? hardware_memory_GB = 15
 
   command {
     cellbender remove-background \
@@ -39,32 +44,33 @@ task run_cellbender_remove_background_gpu {
       --cuda \
       ${"--expected-cells " + expected_cells} \
       ${"--total-droplets-included " + total_droplets_included} \
+      ${"--fpr " + fpr} \
       ${"--model " + model} \
       ${"--low-count-threshold " + low_count_threshold} \
       ${"--epochs " + epochs} \
       ${"--z-dim " + z_dim} \
       ${"--z-layers " + z_layers} \
-      ${"--d-layers " + d_layers} \
-      ${"--p-layers " + p_layers} \
       ${"--empty-drop-training-fraction " + empty_drop_training_fraction} \
       ${"--blacklist-genes " + blacklist_genes} \
       ${"--learning-rate " + learning_rate}
+
+    gsutil -m cp ${sample_name}_out* ${output_directory}/${sample_name}/
   }
 
   output {
     File log = "${sample_name}_out.log"
     File pdf = "${sample_name}_out.pdf"
     File csv = "${sample_name}_out_cell_barcodes.csv"
-    File h5 = "${sample_name}_out.h5"
-    File h5_filt = "${sample_name}_out_filtered.h5"
+    Array[File] h5_array = glob("${sample_name}_out*.h5")  # v2 creates a number of outputs depending on "fpr"
+    String output_dir = "${output_directory}/${sample_name}"
   }
 
   runtime {
     docker: "${docker_image}"
-    bootDiskSizeGb: 20
+    bootDiskSizeGb: hardware_boot_disk_size_GB
     disks: "local-disk ${hardware_disk_size_GB} HDD"
-    memory: "15G"
-    cpu: 4
+    memory: "${hardware_memory_GB}G"
+    cpu: hardware_cpu_count
     zones: "${hardware_zones}"
     gpuCount: 1
     gpuType: "nvidia-tesla-k80"
@@ -82,8 +88,8 @@ workflow cellbender_remove_background {
     File log = run_cellbender_remove_background_gpu.log
     File pdf = run_cellbender_remove_background_gpu.pdf
     File csv = run_cellbender_remove_background_gpu.csv
-    File h5 = run_cellbender_remove_background_gpu.h5
-    File h5_filt = run_cellbender_remove_background_gpu.h5_filt
+    Array[File] h5_array = run_cellbender_remove_background_gpu.h5_array
+    String output_directory = run_cellbender_remove_background_gpu.output_dir
   }
 
 }