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Minor refactor on attachMultiqcReport function. #7129

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merged 3 commits into from
Dec 3, 2024
+19 −21
Merged

Minor refactor on attachMultiqcReport function. #7129

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e4c07f3
Minor refactor on attachMultiqcReport function.
robsyme Nov 30, 2024
3472879
Merge branch 'master' into more-resilient-multiqc-attchments
mirpedrol Dec 3, 2024
60b8816
fix switch brackets
mirpedrol Dec 3, 2024
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40 changes: 19 additions & 21 deletions subworkflows/nf-core/utils_nfcore_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -203,29 +203,26 @@ def logColours(monochrome_logs=true) {
return colorcodes
}

// Return a single report from an object that may be a Path or List
//
// Attach the multiqc report to email
//
def attachMultiqcReport(multiqc_report) {
def mqc_report = null
try {
if (workflow.success) {
mqc_report = multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
if (mqc_report.size() > 1) {
def getSingleReport(multiqc_reports) {
switch (multiqc_reports) {
case Path:
return multiqc_reports
case List:
switch (multiqc_reports.size()) {
case 0:
log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
return null
case 1:
return multiqc_reports.first()
default:
log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
}
mqc_report = mqc_report[0]
return multiqc_reports.first()
}
}
default:
return null
}
catch (Exception msg) {
log.debug(msg)
if (multiqc_report) {
log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
}
}
return mqc_report
}

//
Expand Down Expand Up @@ -279,7 +276,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
email_fields['summary'] = summary << misc_fields

// On success try attach the multiqc report
def mqc_report = attachMultiqcReport(multiqc_report)
def mqc_report = getSingleReport(multiqc_report)

// Check if we are only sending emails on failure
def email_address = email
Expand Down Expand Up @@ -310,7 +307,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
if (email_address) {
try {
if (plaintext_email) {
new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
}
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
Expand Down
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