main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl=2

/**
===============================
Pipeline
===============================

This Pipeline performs ....

### Homepage / git
git@github.com:ikmb/pipeline.git

**/

// Pipeline version

params.version = workflow.manifest.version

def summary = [:]

run_name = ( params.run_name == false) ? "${workflow.sessionId}" : "${params.run_name}"

WorkflowMain.initialise(workflow, params, log)
WorkflowPipeline.initialise( params, log)

include { BACTERIAL_ANNOTATION } from './workflows/bacterial_annotation' params(params)

def multiqc_report = Channel.from([])

workflow {

	BACTERIAL_ANNOTATION()

	multiqc_report = multiqc_report.mix(BACTERIAL_ANNOTATION.out.qc).toList()
}

workflow.onComplete {
  log.info "========================================="
  log.info "Duration:		$workflow.duration"
  log.info "========================================="

  def email_fields = [:]
  email_fields['version'] = workflow.manifest.version
  email_fields['session'] = workflow.sessionId
  email_fields['runName'] = run_name
  email_fields['success'] = workflow.success
  email_fields['dateStarted'] = workflow.start
  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['script_file'] = workflow.scriptFile
  email_fields['launchDir'] = workflow.launchDir
  email_fields['user'] = workflow.userName
  email_fields['Pipeline script hash ID'] = workflow.scriptId
  email_fields['manifest'] = workflow.manifest
  email_fields['summary'] = summary

  email_info = ""
  for (s in email_fields) {
	email_info += "\n${s.key}: ${s.value}"
  }

  def output_d = new File( "${params.outdir}/pipeline_info/" )
  if( !output_d.exists() ) {
      output_d.mkdirs()
  }

  def output_tf = new File( output_d, "pipeline_report.txt" )
  output_tf.withWriter { w -> w << email_info }	

 // make txt template
  def engine = new groovy.text.GStringTemplateEngine()

  def tf = new File("$baseDir/assets/email_template.txt")
  def txt_template = engine.createTemplate(tf).make(email_fields)
  def email_txt = txt_template.toString()

  // make email template
  def hf = new File("$baseDir/assets/email_template.html")
  def html_template = engine.createTemplate(hf).make(email_fields)
  def email_html = html_template.toString()
  
  def subject = "Pipeline finished ($run_name)."

  if (params.email) {

  	def mqc_report = null
  	try {
        	if (workflow.success && !params.skip_multiqc) {
            		mqc_report = multiqc_report.getVal()
            		if (mqc_report.getClass() == ArrayList){
                		//log.warn "[Pipeline] Found multiple reports from process 'multiqc', will use only one"
                		mqc_report = mqc_report[0]
                	}
        	}
    	} catch (all) {
        	log.warn "[IKMB Bacterial-Annotation] Could not attach MultiQC report to summary email"
  	}

	def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.maxMultiqcEmailFileSize.toBytes() ]
	def sf = new File("$baseDir/assets/sendmail_template.txt")	
    	def sendmail_template = engine.createTemplate(sf).make(smail_fields)
    	def sendmail_html = sendmail_template.toString()

	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
        } catch (all) {
          // Catch failures and try with plaintext
          [ 'mail', '-s', subject, params.email ].execute() << email_txt
        }

  }

}