write the commit and timestamp into task_info.yaml (#18)

Author: rcannood

CHANGELOG.md

@@ -26,5 +26,8 @@
 
 * Updated `README.md` (PR #5).
 
+* `run_benchmark`: write the commit the workflow ran from and the launch time into
+  `task_info.yaml`, instead of publishing `_viash.yaml` verbatim (PR #18).
+
 ## BUGFIXES
 

src/workflows/run_benchmark/main.nf

@@ -164,14 +164,23 @@ workflow run_wf {
       metric_configs_file.write(metric_configs_yaml_blob)
 
       // store the task info in a file
-      def viash_file = meta.resources_dir.resolve("_viash.yaml")
+      def task_info = readYaml(meta.resources_dir.resolve("_viash.yaml"))
+      // commitId is null when nextflow runs from a local checkout instead of a revision
+      if (workflow.commitId) {
+        task_info.commit = workflow.commitId
+      }
+      // the launch time -- workflow.complete is only known once the run is over
+      task_info.timestamp = workflow.start.toInstant()
+        .truncatedTo(java.time.temporal.ChronoUnit.SECONDS).toString()
+      def task_info_file = tempFile("task_info.yaml")
+      task_info_file.write(toYamlBlob(task_info))
 
       // create output state
       def new_state = [
         output_dataset_info: dataset_uns_file,
         output_method_configs: method_configs_file,
         output_metric_configs: metric_configs_file,
-        output_task_info: viash_file,
+        output_task_info: task_info_file,
         _meta: states[0]._meta
       ]