Merge pull request nf-core#14 from SciLifeLab/master

Use input channel for output docs rendering; Updated e-mail code
UCL-BLIC · Oct 30, 2017 · f39682d · f39682d
2 parents a2c4e41 + bcf63f5
commit f39682d
Show file tree

Hide file tree

Showing 4 changed files with 59 additions and 21 deletions.
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -4,7 +4,7 @@
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<img src="cid:ngipipelinelogo">
+<img src="cid:ngichipseqlogo">
 
 <h1>NGI-ChIPseq: ChIP-Seq Best Practice v${version}</h1>
 <h2>Run Name: $runName</h2>

diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
@@ -1,38 +1,62 @@
 To: $email
 Subject: $subject
 Mime-Version: 1.0
-Content-Type: multipart/alternative;boundary="ngimethylseqmimeboundary"
+Content-Type: multipart/related;boundary="ngimimeboundary"
 
---ngimethylseqmimeboundary
-Content-Type: text/plain; charset=utf-8
-
-$email_txt
-
---ngimethylseqmimeboundary
+--ngimimeboundary
 Content-Type: text/html; charset=utf-8
 
 $email_html
 
---ngimethylseqmimeboundary
+--ngimimeboundary
 Content-Type: image/png;name="NGI-ChIPseq_logo.png"
 Content-Transfer-Encoding: base64
-Content-ID: <ngipipelinelogo>
+Content-ID: <ngichipseqlogo>
 Content-Disposition: inline; filename="NGI-ChIPseq_logo.png"
 
-<% out << new File("$baseDir/assets/NGI-ChIPseq_logo.png").bytes.encodeBase64().toString() %>
-
---ngimethylseqmimeboundary
+<% out << new File("$baseDir/assets/NGI-ChIPseq_logo.png").
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' ) %>
+
+--ngimimeboundary
 Content-Type: image/png;name="SciLifeLab_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <scilifelablogo>
 Content-Disposition: inline; filename="SciLifeLab_logo.png"
 
-<% out << new File("$baseDir/assets/SciLifeLab_logo.png").bytes.encodeBase64().toString() %>
-
---ngimethylseqmimeboundary
+<% out << new File("$baseDir/assets/SciLifeLab_logo.png").
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' ) %>
+
+--ngimimeboundary
 Content-Type: image/png;name="NGI_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <ngilogo>
 Content-Disposition: inline; filename="NGI_logo.png"
 
-<% out << new File("$baseDir/assets/NGI_logo.png").bytes.encodeBase64().toString() %>
+<% out << new File("$baseDir/assets/NGI_logo.png").
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' ) %>
+
+--ngimimeboundary--
diff --git a/docs/usage.md b/docs/usage.md
@@ -154,6 +154,9 @@ The output directory where the results will be saved.
 ### `--email`
 Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to speicfy this on the command line for every run.
 
+### `--plaintext_email`
+Set to receive plain-text e-mails instead of HTML formatted.
+
 ### `-name`
 Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
 

diff --git a/main.nf b/main.nf
@@ -54,6 +54,7 @@ params.saveAlignedIntermediates = false
 params.broad = false
 params.outdir = './results'
 params.email = false
+params.plaintext_email = false
 
 // Validate inputs
 macsconfig = file(params.macsconfig)
@@ -86,6 +87,7 @@ params.three_prime_clip_r2 = 0
 // Config / R locations
 params.multiqc_config = "$baseDir/conf/multiqc_config.yaml"
 multiqc_config = file(params.multiqc_config)
+output_docs = file("$baseDir/docs/output.md")
 params.rlocation = false
 if (params.rlocation){
     nxtflow_libs = file(params.rlocation)
@@ -612,14 +614,15 @@ process output_documentation {
 
     input:
     val prefix from multiqc_prefix
+    file output from output_docs
 
     output:
     file "results_description.html"
 
     script:
     def rlocation = params.rlocation ?: ''
     """
-    markdown_to_html.r $baseDir/docs/output.md results_description.html $rlocation
+    markdown_to_html.r $output results_description.html $rlocation
     """
 }
 
@@ -678,17 +681,25 @@ workflow.onComplete {
     // Send the HTML e-mail
     if (params.email) {
         try {
+          if( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
           // Try to send HTML e-mail using sendmail
           [ 'sendmail', '-t' ].execute() << sendmail_html
-          log.debug "[NGI-ChIPseq] Sent summary e-mail using sendmail"
+          log.info "[NGI-ChIPseq] Sent summary e-mail to $params.email (sendmail)"
         } catch (all) {
           // Catch failures and try with plaintext
           [ 'mail', '-s', subject, params.email ].execute() << email_txt
-          log.debug "[NGI-ChIPseq] Sendmail failed, failing back to sending summary e-mail using mail"
+          log.info "[NGI-ChIPseq] Sent summary e-mail to $params.email (mail)"
         }
-        log.info "[NGI-ChIPseq] Sent summary e-mail to $params.email"
     }
 
+    // Switch the embedded MIME images with base64 encoded src
+    ngichipseqlogo = new File("$baseDir/assets/NGI-ChIPseq_logo.png").bytes.encodeBase64().toString()
+    scilifelablogo = new File("$baseDir/assets/SciLifeLab_logo.png").bytes.encodeBase64().toString()
+    ngilogo = new File("$baseDir/assets/NGI_logo.png").bytes.encodeBase64().toString()
+    email_html = email_html.replaceAll(~/cid:ngichipseqlogo/, "data:image/png;base64,$ngichipseqlogo")
+    email_html = email_html.replaceAll(~/cid:scilifelablogo/, "data:image/png;base64,$scilifelablogo")
+    email_html = email_html.replaceAll(~/cid:ngilogo/, "data:image/png;base64,$ngilogo")
+
     // Write summary e-mail HTML to a file
     def output_d = new File( "${params.outdir}/Documentation/" )
     if( !output_d.exists() ) {