Move version to NfcoreTemplate

nf-core · Nov 16, 2022 · 939e2ba · 939e2ba
1 parent 000ef79
commit 939e2ba
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Showing 2 changed files with 24 additions and 23 deletions.
diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
@@ -32,6 +32,25 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Generate version string
+    //
+    public static String version(workflow) {
+        String version_string = ""
+
+        if (workflow.manifest.version) {
+            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+            version_string += "${prefix_v}${workflow.manifest.version}"
+        }
+
+        if (workflow.commitId) {
+            def git_shortsha = workflow.commitId.substring(0, 7)
+            version_string += "-g${git_shortsha}"
+        }
+
+        return version_string
+    }
+
     //
     // Construct and send completion email
     //
@@ -61,7 +80,7 @@ class NfcoreTemplate {
         misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
         def email_fields = [:]
-        email_fields['version']      = workflow.manifest.version
+        email_fields['version']      = NfcoreTemplate.version(workflow)
         email_fields['runName']      = workflow.runName
         email_fields['success']      = workflow.success
         email_fields['dateComplete'] = workflow.complete
@@ -170,7 +189,7 @@ class NfcoreTemplate {
         misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
 
         def msg_fields = [:]
-        msg_fields['version']      = workflow.manifest.version
+        msg_fields['version']      = NfcoreTemplate.version(workflow)
         msg_fields['runName']      = workflow.runName
         msg_fields['success']      = workflow.success
         msg_fields['dateComplete'] = workflow.complete
@@ -297,6 +316,7 @@ class NfcoreTemplate {
     //
     public static String logo(workflow, monochrome_logs) {
         Map colors = logColours(monochrome_logs)
+        String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
             """\n
             ${dashedLine(monochrome_logs)}{% if branded %}
@@ -305,7 +325,7 @@ class NfcoreTemplate {
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
             ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
                                                     ${colors.green}`._,._,\'${colors.reset}{% endif %}
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()
         )

diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -35,25 +35,6 @@ class WorkflowMain {
         return help_string
     }
 
-    //
-    // Generate version string
-    //
-    public static String version(workflow, params, log) {
-        String version_string = ""
-
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
-        }
-
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
-        }
-
-        return version_string
-    }
-
     //
     // Generate parameter summary log string
     //
@@ -78,7 +59,7 @@ class WorkflowMain {
 
         // Print workflow version and exit on --version
         if (params.version) {
-            String workflow_version = version(workflow, params, log)
+            String workflow_version = NfcoreTemplate.version(workflow)
             log.info "${workflow.manifest.name} ${workflow_version}"
             System.exit(0)
         }