Merge pull request #140 from sanger-tol/mm49_pre_tag

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sanger-tol · Sep 15, 2023 · 87d2635 · 87d2635
2 parents 7c1b69e + e9dd94d
commit 87d2635
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Showing 2 changed files with 11 additions and 6 deletions.
diff --git a/lib/TreeValProject.groovy b/lib/TreeValProject.groovy
@@ -1,3 +1,6 @@
+import java.time.OffsetDateTime;
+import java.time.Duration;
+
 class TreeValProject {
     //
     // Generates a small summary containing context for the input files
@@ -7,13 +10,15 @@ class TreeValProject {
 
     public static void summary(workflow, params, metrics, log) {
 
+        def date_completed = OffsetDateTime.now()
+
         def input_data = [:]
         input_data['version']           = NfcoreTemplate.version( workflow )
         input_data['runName']           = workflow.runName
         input_data['session_id']        = workflow.sessionId
-        input_data['duration']          = 'CANNOT BE CALCULATED'
+        input_data['duration']          = Duration.between( workflow.start, date_completed ).toSeconds()
         input_data['DateStarted']       = workflow.start
-        input_data['DateCompleted']     = new Date().format("yyyy-MM-dd HH:mm:ss.SSSZ")
+        input_data['DateCompleted']     = date_completed
         input_data['entry']             = params.entry
 
         input_data['input_yaml']        = params.input

diff --git a/subworkflows/local/hic_mapping.nf b/subworkflows/local/hic_mapping.nf
@@ -154,12 +154,12 @@ workflow HIC_MAPPING {
     // LOGIC: HIRES IS TOO INTENSIVE FOR RUNNING IN GITHUB CI SO THIS STOPS IT RUNNING
     //
     if ( params.config_profile_name ) {
-        github = params.config_profile_name
+        config_profile_name = params.config_profile_name
     } else {
-        github = 'Local'
+        config_profile_name = 'Local'
     }
 
-    if ( !github.contains('GitHub') ) {
+    if ( !config_profile_name.contains('GitHub') ) {
         //
         // MODULE: GENERATE PRETEXT MAP FROM MAPPED BAM FOR HIGH RES
         //
@@ -211,7 +211,7 @@ workflow HIC_MAPPING {
     //
     // LOGIC: SECTION ONLY NEEDED FOR TREEVAL VISUALISATION, NOT RAPID ANALYSIS
     //
-    if (workflow_setting == 'FULL' && !github.contains('GitHub')) {
+    if (workflow_setting == 'FULL' && !config_profile_name.contains('GitHub')) {
         //
         // LOGIC: PREPARE JUICER TOOLS INPUT
         //