Merge pull request #399 from jfy133/tsv-input

Fixing email stuff

Author: jfy133

main.nf

@@ -212,7 +212,7 @@ def helpMessage() {
       --max_cpus                    Maximum number of CPUs to use for each step of the pipeline. Should be in form e.g. Default: '${params.max_cpus}'
       --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
       --plaintext_email             Receive plain text emails rather than HTML
-      --maxMultiqcEmailFileSize     Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
+      --max_multiqc_email_size     Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
       
     For a full list and more information of available parameters, consider the documentation (https://github.com/nf-core/eager/).
     """.stripIndent()
@@ -2634,7 +2634,7 @@ process multiqc {
     file workflow_summary from ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml")
 
     output:
-    file "*multiqc_report.html" into multiqc_report
+    file "*multiqc_report.html" into ch_multiqc_report
     file "*_data"
 
     script:
@@ -2725,7 +2725,11 @@ workflow.onComplete {
             log.info "[nf-core/eager] Sent summary e-mail to $email_address (sendmail)"
         } catch (all) {
             // Catch failures and try with plaintext
-            [ 'mail', '-s', subject, email_address ].execute() << email_txt
+            if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
+              [ 'mail', '-s', subject, email_address, '-A', mqc_report ].execute() << email_txt 
+            } else {
+              [ 'mail', '-s', subject, email_address ].execute() << email_txt 
+            }
             log.info "[nf-core/eager] Sent summary e-mail to $email_address (mail)"
         }
     }