Merge branch 'master' into BenchmarkCNV

.dockstore.yml

@@ -88,4 +88,10 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.wdl
    testParameterFiles:
-   - /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.inputs.json
+   - /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.inputs.json
+ - name: checkBaitSetName_dev
+   subclass: WDL
+   primaryDescriptorPath: /checkBaitSetName/checkBaitSetName.dev.wdl
+   testParameterFiles:
+    - /checkBaitSetName/checkBaitSetName.dev.inputs.json
+

checkBaitSetName/checkBaitSetName.dev.inputs.json

@@ -0,0 +1,6 @@
+{
+  "checkBaitSetName.compareBaitSetName.target_intervals": "File",
+  "checkBaitSetName.compareBaitSetName.bait_intervals": "File? (optional)",
+  "checkBaitSetName.compareBaitSetName.fail_task": "Boolean",
+  "checkBaitSetName.compareBaitSetName.bait_set": "String"
+}

checkBaitSetName/checkBaitSetName.dev.wdl

@@ -0,0 +1,54 @@
+workflow checkBaitSetName{
+  call compareBaitSetName
+
+  output {
+  	String mismatch_message = compareBaitSetName.mismatch_message
+    Int? bait_mismatch = compareBaitSetName.bait_mismatch
+  }
+}
+
+task compareBaitSetName {
+  String bait_set
+  Boolean fail_task
+  File target_intervals
+  File? bait_intervals
+  String target_intervals_name = basename(target_intervals)
+  String bait_intervals_name = if defined(bait_intervals) then basename(select_first([bait_intervals])) else bait_set + "."
+
+  command <<<
+python <<CODE
+import sys
+target_correct = "${target_intervals_name}".startswith("${bait_set}.")
+bait_correct = "${bait_intervals_name}".startswith("${bait_set}.")
+if not target_correct and not bait_correct:
+  print("Bait and target intervals do not match the bait_set.")
+  open("set_mismatch.txt", 'w').write("1")
+  sys.stderr.write("1")
+elif not target_correct:
+  print("Target intervals do not match the bait_set.")
+  open("set_mismatch.txt", 'w').write("1")
+  sys.stderr.write("1")
+elif not bait_correct:
+  print("Bait intervals do not match the bait_set.")
+  open("set_mismatch.txt", 'w').write("1")
+  sys.stderr.write("1")
+else:
+  print("bait_set matches the provided intervals.")
+  open("set_mismatch.txt", 'w').write("0")
+CODE
+  >>>
+
+  output {
+    String mismatch_message = read_string(stdout())
+    Int bait_mismatch = read_int("set_mismatch.txt")
+  }
+
+  runtime {
+    docker: "python:3"
+    memory: "2 GB"
+    disks: "local-disk 10 HDD"
+    preemptible: 1
+    maxRetries: 0
+    failOnStderr: fail_task
+  }
+}