-
+
NGI-ChIPseq: ChIP-Seq Best Practice v${version}
Run Name: $runName
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index cfd81544..a76e8665 100644
--- 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
$email_html
---ngimethylseqmimeboundary
+--ngimimeboundary
Content-Type: image/png;name="NGI-ChIPseq_logo.png"
Content-Transfer-Encoding: base64
-Content-ID:
+Content-ID:
Content-Disposition: inline; filename="NGI-ChIPseq_logo.png"
-<% out << new File("$baseDir/assets/NGI-ChIPseq_logo.png").bytes.encodeBase64().toString() %>
-
---ngimethylseqmimeboundary
+<% out << new File("$baseDir/assets/NGI-ChIPseq_logo.png").
+ bytes.
+ encodeBase64().
+ toString().
+ tokenize( '\n' )*.
+ toList()*.
+ collate( 76 )*.
+ collect { it.join() }.
+ flatten().
+ join( '\n' ) %>
+
+--ngimimeboundary
Content-Type: image/png;name="SciLifeLab_logo.png"
Content-Transfer-Encoding: base64
Content-ID:
Content-Disposition: inline; filename="SciLifeLab_logo.png"
-<% out << new File("$baseDir/assets/SciLifeLab_logo.png").bytes.encodeBase64().toString() %>
-
---ngimethylseqmimeboundary
+<% out << new File("$baseDir/assets/SciLifeLab_logo.png").
+ bytes.
+ encodeBase64().
+ toString().
+ tokenize( '\n' )*.
+ toList()*.
+ collate( 76 )*.
+ collect { it.join() }.
+ flatten().
+ join( '\n' ) %>
+
+--ngimimeboundary
Content-Type: image/png;name="NGI_logo.png"
Content-Transfer-Encoding: base64
Content-ID:
Content-Disposition: inline; filename="NGI_logo.png"
-<% out << new File("$baseDir/assets/NGI_logo.png").bytes.encodeBase64().toString() %>
+<% out << new File("$baseDir/assets/NGI_logo.png").
+ bytes.
+ encodeBase64().
+ toString().
+ tokenize( '\n' )*.
+ toList()*.
+ collate( 76 )*.
+ collect { it.join() }.
+ flatten().
+ join( '\n' ) %>
+
+--ngimimeboundary--
diff --git a/docs/usage.md b/docs/usage.md
index 3c310750..120a9915 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -154,6 +154,9 @@ The output directory where the results will be saved.
### `--email`
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to speicfy this on the command line for every run.
+### `--plaintext_email`
+Set to receive plain-text e-mails instead of HTML formatted.
+
### `-name`
Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
diff --git a/main.nf b/main.nf
index 9fd48645..60a1a1ae 100755
--- a/main.nf
+++ b/main.nf
@@ -54,6 +54,7 @@ params.saveAlignedIntermediates = false
params.broad = false
params.outdir = './results'
params.email = false
+params.plaintext_email = false
// Validate inputs
macsconfig = file(params.macsconfig)
@@ -86,6 +87,7 @@ params.three_prime_clip_r2 = 0
// Config / R locations
params.multiqc_config = "$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)
@@ -612,6 +614,7 @@ process output_documentation {
input:
val prefix from multiqc_prefix
+ file output from output_docs
output:
file "results_description.html"
@@ -619,7 +622,7 @@ process output_documentation {
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() ) {