Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (#6975)

broadinstitute · Jan 18, 2023 · 32f8a90 · 32f8a90
1 parent 505a370
commit 32f8a90
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Showing 6 changed files with 290 additions and 4,741 deletions.
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
@@ -1,3 +1,4 @@
 {
-  "wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.tile_db_header.vcf"
+  "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx"
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -1,11 +1,20 @@
+version 1.0
+
 task check_if_localized_as_symlink {
-  File reference_file_input
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+  }
+  String broad_input_symlink = "broad_input_symlink.txt"
+  String nirvana_input_symlink = "nirvana_input_symlink.txt"
   command {
-     # print true if file is a symlink, otherwise print false
-     if test -h ${reference_file_input}; then echo "true"; else echo "false"; fi;
+    # Print true if input is a symlink, otherwise print false.
+    if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
+    if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
   }
   output {
-    Boolean is_symlink = read_boolean(stdout())
+    Boolean is_broad_input_symlink = read_boolean("~{broad_input_symlink}")
+    Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -14,8 +23,17 @@ task check_if_localized_as_symlink {
 }
 
 workflow wf_reference_disk_test {
-  call check_if_localized_as_symlink
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+  }
+  call check_if_localized_as_symlink {
+    input:
+      broad_reference_file_input = broad_reference_file_input,
+      nirvana_reference_file_input = nirvana_reference_file_input
+  }
   output {
-     Boolean is_input_file_a_symlink = check_if_localized_as_symlink.is_symlink
+    Boolean is_broad_input_file_a_symlink = check_if_localized_as_symlink.is_broad_input_symlink
+    Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
   }
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
@@ -11,5 +11,6 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
@@ -11,5 +11,6 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": true
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
@@ -11,5 +11,6 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
 }