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main.nf
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main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
/**
===============================
Pipeline
===============================
This Pipeline performs ....
### Homepage / git
[email protected]: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)
WorkflowHla.initialise( params, log)
params.fasta = file(params.genomes[ "hg38" ].fasta, checkIfExists: true)
params.dict = file(params.genomes[ "hg38" ].dict, checkIfExists: true)
params.fai = file(params.genomes[ "hg38" ].fasta + ".fai", checkIfExists: true)
include { HLA } from './workflows/hla'
multiqc_report = Channel.from([])
log.info "------------------------------------------"
log.info "IKMB HLA Pipeline v${params.version}"
log.info "------------------------------------------"
log.info "${workflow.manifest.description}"
log.info "Nextflow Version: $workflow.nextflow.version"
log.info "Tools requested: ${params.tools}"
log.info "Genes to analyse: ${params.hla_genes.join(',')}"
log.info "------------------------------------------"
workflow {
HLA()
multiqc_report = multiqc_report.mix(HLA.out.qc)
}
workflow.onComplete {
log.info "========================================="
log.info "Duration: $workflow.duration"
log.info "========================================="
def email_fields = [:]
email_fields['version'] = workflow.manifest.version
email_fields['session'] = workflow.sessionId
email_fields['runName'] = run_name
email_fields['Samples'] = params.samples
email_fields['success'] = workflow.success
email_fields['dateStarted'] = workflow.start
email_fields['dateComplete'] = workflow.complete
email_fields['duration'] = workflow.duration
email_fields['exitStatus'] = workflow.exitStatus
email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
email_fields['errorReport'] = (workflow.errorReport ?: 'None')
email_fields['commandLine'] = workflow.commandLine
email_fields['projectDir'] = workflow.projectDir
email_fields['script_file'] = workflow.scriptFile
email_fields['launchDir'] = workflow.launchDir
email_fields['user'] = workflow.userName
email_fields['Pipeline script hash ID'] = workflow.scriptId
email_fields['manifest'] = workflow.manifest
email_fields['summary'] = summary
email_info = ""
for (s in email_fields) {
email_info += "\n${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 ($run_name)."
if (params.email) {
def mqc_report = null
try {
if (workflow.success && !params.skip_multiqc) {
mqc_report = multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList){
log.warn "[Pipeline] Found multiple reports from process 'multiqc', will use only one"
mqc_report = mqc_report[0]
}
}
} catch (all) {
log.warn "[IKMB HLA] Could not attach MultiQC report to summary email"
}
def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$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
}
}
}