Added Slack/Teams notifications

assets/slackreport.json

@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "TalusBio/nf-encyclopedia - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}

lib/TalusTemplate.groovy

@@ -41,4 +41,53 @@ class TalusTemplate {
         def email_html = html_template.toString()
         return [subject, email_html]
     }
+
+    //
+    // Construct and send a notification to a web server as JSON
+    // e.g. Microsoft Teams and Slack
+    //
+    public static void IM_notification(workflow, params, projectDir) {
+        def hook_url = params.hook_url
+        def misc_fields = [:]
+        misc_fields['start']                                = workflow.start
+        misc_fields['complete']                             = workflow.complete
+        misc_fields['scriptfile']                           = workflow.scriptFile
+        misc_fields['scriptid']                             = workflow.scriptId
+        if (workflow.repository) misc_fields['repository']  = workflow.repository
+        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+        if (workflow.revision)   misc_fields['revision']    = workflow.revision
+        misc_fields['nxf_version']                          = workflow.nextflow.version
+        misc_fields['nxf_build']                            = workflow.nextflow.build
+        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+        def summary = [:]
+        def msg_fields = [:]
+        msg_fields['runName']      = workflow.runName
+        msg_fields['success']      = workflow.success
+        msg_fields['dateComplete'] = workflow.complete
+        msg_fields['duration']     = workflow.duration
+        msg_fields['exitStatus']   = workflow.exitStatus
+        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+        msg_fields['projectDir']   = workflow.projectDir
+        msg_fields['summary']      = summary << misc_fields
+
+        // Render the JSON template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        // Different JSON depending on the service provider
+        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+        def hf            = new File("$projectDir/assets/${json_path}")
+        def json_template = engine.createTemplate(hf).make(msg_fields)
+        def json_message  = json_template.toString()
+
+        // POST
+        def post = new URL(hook_url).openConnection();
+        post.setRequestMethod("POST")
+        post.setDoOutput(true)
+        post.setRequestProperty("Content-Type", "application/json")
+        post.getOutputStream().write(json_message.getBytes("UTF-8"));
+        def postRC = post.getResponseCode();
+    }
 }

main.nf

@@ -31,6 +31,16 @@ def email() {
 }
 
 
+//
+// Used for Slack notifications
+//
+def slack() {
+    if (params.hook_url) {
+        TalusTemplate.IM_notification(workflow, params, projectDir)
+    }
+}
+
+
 //
 // Use the DLIB when the ELIB is unavailable.
 //
@@ -133,4 +143,7 @@ workflow dummy {
 }
 
 // Email notifications:
-workflow.onComplete { email() }
+workflow.onComplete {
+    email()
+    slack()
+}

nextflow.config

@@ -54,6 +54,7 @@ params {
     report_dir = 'reports' /** \type{str} Where reports will be saved. */
     mzml_dir = 'mzml'      /** \type{str} Where mzML files will be saved. */
     email = null           /** \type{str} An email to alert on completion. */
+    hook_url = null        /** \type{str} A URL for Slack notifications */
 
     /** \group{Grouping Parameters} */
     /** \type{boolean}