main.nf

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

/**
===============================
Dragen Variant Calling Pipeline
===============================

This Pipeline performs variant calling
using Illumina Dragen

### Homepage / git
git@github.com:ikmb/dragen-variant-calling.git
### Implementation
Re-Implemented in Q1 2023

Author: Marc P. Hoeppner, m.hoeppner@ikmb.uni-kiel.de

**/

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

include { DRAGEN_VARIANT_CALLING } from "./workflows/dragen"

// *********************
// Collect summary
// **********************
def summary = [:]
summary['DragenReference']  = params.dragen_ref_dir
if (params.kit) {
	summary['Kit']          = params.kit
}

// ***********************
// The main workflow
// ***********************

def multiqc_report = Channel.from([])

workflow {

        DRAGEN_VARIANT_CALLING()
        multiqc_report = multiqc_report.mix(DRAGEN_VARIANT_CALLING.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'] = params.run_name
        email_fields['Samples'] = params.samples
        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_fields['intervalPadding'] = params.interval_padding

        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 = "Dragen analysis finished ($params.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 "[IKMB DragenVariantCalling] Found multiple reports from process 'multiqc', will use only one"
                                        mqc_report = mqc_report[-1]
                                }
                        }
                } catch (all) {
                        log.warn "[IKMB DragenVariantCalling] 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', '-f no-reply@ikmb.uni-kiel.de',  '-t' ].execute() << sendmail_html
                } catch (all) {
                        // Catch failures and try with plaintext
                        [ 'mail', '-s', subject, params.email ].execute() << email_txt
                
                }
        }
}