validate typescript expression using cwl-ica

umccr · Feb 18, 2025 · c0e4f57 · c0e4f57
1 parent 5c8a6d5
commit c0e4f57
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Showing 5 changed files with 448 additions and 428 deletions.
diff --git a/typescript-expressions/dragen-tools/4.0.3/dragen-tools__4.0.3.cwljs b/typescript-expressions/dragen-tools/4.0.3/dragen-tools__4.0.3.cwljs
@@ -667,3 +667,9 @@ function generate_ora_mount_points(input_run, output_directory_path, sample_id_l
     /*  @ts-ignore Type '{ entryname:string; entry:FileProperties; }[]' is not assignable to type 'DirentProperties[]' */
     return e;
 }
+function get_contamination_dir() {
+    /*
+    Hardcoded contamination directory in dragen
+    */
+    return "/opt/edico/config/";
+}
diff --git a/typescript-expressions/dragen-tools/4.0.3/dragen-tools__4.0.3.js b/typescript-expressions/dragen-tools/4.0.3/dragen-tools__4.0.3.js
@@ -35,6 +35,7 @@ exports.find_fastq_files_in_directory_recursively_with_regex = find_fastq_files_
 exports.get_rgsm_value_from_fastq_file_name = get_rgsm_value_from_fastq_file_name;
 exports.get_lane_value_from_fastq_file_name = get_lane_value_from_fastq_file_name;
 exports.generate_ora_mount_points = generate_ora_mount_points;
+exports.get_contamination_dir = get_contamination_dir;
 // Author: Alexis Lucattini
 // For assistance on generation of typescript expressions
 // In CWL, please visit our wiki page at https://github.com/umccr/cwl-ica/wiki/TypeScript
@@ -705,3 +706,9 @@ function generate_ora_mount_points(input_run, output_directory_path, sample_id_l
     // @ts-ignore Type '{ entryname: string; entry: FileProperties; }[]' is not assignable to type 'DirentProperties[]'
     return e;
 }
+function get_contamination_dir() {
+    /*
+    Hardcoded contamination directory in dragen
+    */
+    return "/opt/edico/config/";
+}
diff --git a/typescript-expressions/dragen-tools/4.0.3/dragen-tools__4.0.3.ts b/typescript-expressions/dragen-tools/4.0.3/dragen-tools__4.0.3.ts
@@ -777,4 +777,11 @@ export function generate_ora_mount_points(input_run: IDirectory, output_director
     // Return the dirent
     // @ts-ignore Type '{ entryname: string; entry: FileProperties; }[]' is not assignable to type 'DirentProperties[]'
     return e;
+}
+
+export function get_contamination_dir(): string {
+    /*
+    Hardcoded contamination directory in dragen
+    */
+    return "/opt/edico/config/";
 }
diff --git a/typescript-expressions/dragen-tools/4.0.3/tests/summary.txt b/typescript-expressions/dragen-tools/4.0.3/tests/summary.txt
@@ -1,4 +1,4 @@
-# Test started at 2024-11-20T21:05:15+11:00
+# Test started at 2025-02-18T15:47:25+11:00
 
 PASS tests/dragen-tools__4.0.3.test.js
   ● Console
@@ -12,7 +12,7 @@ PASS tests/dragen-tools__4.0.3.test.js
         groups: undefined
       ]
 
-      at log (dragen-tools__4.0.3.js:639:17)
+      at log (dragen-tools__4.0.3.js:640:17)
 
     console.log
       [
@@ -23,7 +23,7 @@ PASS tests/dragen-tools__4.0.3.test.js
         groups: undefined
       ]
 
-      at log (dragen-tools__4.0.3.js:639:17)
+      at log (dragen-tools__4.0.3.js:640:17)
 
 FAIL tests/dragen-tools__4.0.3.test.ts
   ● Test suite failed to run
@@ -35,15 +35,15 @@ FAIL tests/dragen-tools__4.0.3.test.ts
 
 
 =============================== Coverage summary ===============================
-Statements   : 84.64% ( 248/293 )
+Statements   : 84.4% ( 249/295 )
 Branches     : 69.71% ( 99/142 )
-Functions    : 58.33% ( 21/36 )
-Lines        : 83.27% ( 224/269 )
+Functions    : 56.75% ( 21/37 )
+Lines        : 83.02% ( 225/271 )
 ================================================================================
 Test Suites: 1 failed, 1 passed, 2 total
 Tests:       16 passed, 16 total
 Snapshots:   0 total
-Time:        1.838 s
+Time:        1.395 s
 Ran all test suites.
-# Test completed at 2024-11-20T21:05:18+11:00
+# Test completed at 2025-02-18T15:47:28+11:00