Created
June 14, 2017 15:16
-
-
Save ewels/2da5023f0b045f92434ad0cb5ad7e8aa to your computer and use it in GitHub Desktop.
NextFlow Multipart HTML Emails
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <html> | |
| <head> | |
| <title>NextFlow Pipeline Complete</title> | |
| </head> | |
| <body> | |
| <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;"> | |
| <h1>NextFlow Pipeline Complete</h1> | |
| <h2>Run Name: $runName</h2> | |
| <% if (success){ | |
| out << """ | |
| <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;"> | |
| NGI-RNAseq execution completed successfully! | |
| </div> | |
| """ | |
| } else { | |
| out << """ | |
| <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;"> | |
| <h4 style="margin-top:0; color: inherit;">NGI-RNAseq execution completed unsuccessfully!</h4> | |
| <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p> | |
| <p>The full error message was:</p> | |
| <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre> | |
| </div> | |
| """ | |
| } %> | |
| <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p> | |
| <p>The command used to launch the workflow was as follows:</p> | |
| <pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre> | |
| <h3>Pipeline Configuration:</h3> | |
| <table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;"> | |
| <tbody style="border-bottom: 1px solid #ddd;"> | |
| <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %> | |
| </tbody> | |
| </table> | |
| <p>To find out more information about NextFlow, see <a href="http://nextflow.io">http://nextflow.io</a></p> | |
| <hr style="height: 3px; padding: 0; margin: 24px 0; background-color: #e1e4e8; border: 0;"> | |
| <img src="cid:$nf_logo_cid"> | |
| </div> | |
| </body> | |
| </html> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ============================ | |
| NextFlow Pipeline Complete | |
| ============================ | |
| Run Name: $runName | |
| <% if (success){ | |
| out << "NGI-RNAseq execution completed successfully!" | |
| } else { | |
| out << """#################################################### | |
| ## NGI-RNAseq execution completed unsuccessfully! ## | |
| #################################################### | |
| The exit status of the task that caused the workflow execution to fail was: $exitStatus. | |
| The full error message was: | |
| ${errorReport} | |
| """ | |
| } %> | |
| The workflow was completed at $dateComplete (duration: $duration) | |
| The command used to launch the workflow was as follows: | |
| $commandLine | |
| Pipeline Configuration: | |
| ----------------------- | |
| <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> | |
| -- | |
| To find out more information about NextFlow, see http://nextflow.io |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/usr/bin/env nextflow | |
| /* | |
| vim: syntax=groovy | |
| -*- mode: groovy;-*- | |
| */ | |
| // Import some Java packages that we need for e-mail | |
| import javax.mail.internet.* | |
| import javax.mail.* | |
| import javax.activation.* | |
| // Set up the default parameters | |
| params.email = false | |
| params.email_protocol = "smtp" | |
| params.email_host = "localhost" | |
| params.email_port = "25" | |
| // Dummy channel to get the pipeline to run | |
| cheers=Channel.from "Bonjour", "Ciao","Hello","Hola" | |
| process sayHello { | |
| input: val x from cheers | |
| script: "echo $x world!" | |
| } | |
| // Run when pipeline is complete | |
| workflow.onComplete { | |
| // Set up the e-mail variables | |
| def email_fields = [:] | |
| email_fields['version'] = version | |
| email_fields['runName'] = workflow.runName | |
| email_fields['success'] = workflow.success | |
| email_fields['dateComplete'] = workflow.complete | |
| email_fields['duration'] = workflow.duration | |
| email_fields['exitStatus'] = workflow.exitStatus | |
| email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') | |
| email_fields['errorReport'] = (workflow.errorReport ?: 'None') | |
| email_fields['commandLine'] = workflow.commandLine | |
| email_fields['projectDir'] = workflow.projectDir | |
| email_fields['summary'] = [:] | |
| email_fields['summary']['Date Started'] = workflow.start | |
| email_fields['summary']['Date Completed'] = workflow.complete | |
| email_fields['summary']['Nextflow Version'] = workflow.nextflow.version | |
| email_fields['summary']['Nextflow Build'] = workflow.nextflow.build | |
| email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp | |
| email_fields['summary']['Pipeline script file path'] = workflow.scriptFile | |
| email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId | |
| // MIME image cid (for NF logo) | |
| email_fields['nf_logo_cid'] = "nflogo" | |
| // Render the e-mail TXT template | |
| def engine = new groovy.text.GStringTemplateEngine() | |
| def tf = new File("$baseDir/email_template.txt") | |
| def txt_template = engine.createTemplate(tf).make(email_fields) | |
| def email_txt = txt_template.toString() | |
| // Render the e-mail HTML template | |
| def hf = new File("$baseDir/email_template.html") | |
| def html_template = engine.createTemplate(hf).make(email_fields) | |
| def email_html = html_template.toString() | |
| if(params.email){ | |
| try { | |
| // Configure how to send the mail | |
| Properties mprops = new Properties(); | |
| mprops.setProperty("mail.transport.protocol", params.email_protocol); | |
| mprops.setProperty("mail.host", params.email_host); | |
| mprops.setProperty("mail.smtp.port", params.email_port); | |
| Session lSession = Session.getDefaultInstance(mprops); | |
| new MimeMessage(lSession).with { msg -> | |
| // Create MultiPart mail | |
| Multipart multiPart = new MimeMultipart("related"); | |
| // txt part | |
| /* | |
| NB: Can't get this to work as well as the embedded image | |
| if wanted, remove the NF Logo section and change the above | |
| line to: Multipart multiPart = new MimeMultipart("alternative"); | |
| */ | |
| // MimeBodyPart textPart = new MimeBodyPart(); | |
| // textPart.setText(email_txt, "utf-8"); | |
| // multiPart.addBodyPart(textPart); | |
| // html part | |
| MimeBodyPart htmlPart = new MimeBodyPart(); | |
| htmlPart.setContent(email_html, "text/html; charset=utf-8"); | |
| multiPart.addBodyPart(htmlPart); | |
| // NF Logo | |
| MimeBodyPart nfLogo = new MimeBodyPart(); | |
| nfLogo.attachFile("$baseDir/NF_logo.png"); | |
| nfLogo.setContentID("<" + email_fields['nf_logo_cid'] + ">"); | |
| nfLogo.setDisposition(MimeBodyPart.INLINE); | |
| multiPart.addBodyPart(nfLogo); | |
| // Build the e-mail | |
| setRecipients(MimeMessage.RecipientType.TO, new InternetAddress(params.email)); | |
| setFrom(new InternetAddress(params.email)); | |
| setSubject("NextFlow - Pipeline Complete: " + workflow.runName); | |
| setContent(multiPart); | |
| // Send the e-mail | |
| Transport transporter = lSession.getTransport("smtp"); | |
| transporter.connect(); | |
| transporter.send(msg); | |
| // Celebrate! | |
| log.info "Sent NextFlow summary e-mail to $params.email" | |
| } | |
| } catch( MessagingException mex ) { | |
| log.error "There was an error whilst sending the summary e-mail" | |
| mex.printStackTrace() | |
| } | |
| } else { | |
| log.warn "No e-mail address set - skipping summary e-mail" | |
| } | |
| } | |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Save NextFlow logo as this file. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment