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fix issue 9424: MultiQC report handling for AWS batch with S3 workDir #9455

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fix issue 9424: MultiQC report handling for AWS batch with S3 workDir #9455

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22 changes: 21 additions & 1 deletion subworkflows/nf-core/utils_nfcore_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -276,6 +276,26 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// On success try attach the multiqc report
def mqc_report = getSingleReport(multiqc_report)

// Fix issue https://github.com/nf-core/modules/issues/9424 when running on AWS batch with S3 workDir. mqc_report is not downloaded locally.
def mqc_report_file = null

if (mqc_report != null) {
try {
// Check if we're using S3 for the report file and need to download it so the head node can access it
if (mqc_report.toUriString().startsWith('s3://')) {
def tempFile = file("${workflow.launchDir}/multiqc_report_${workflow.sessionId}.html")
mqc_report.copyTo(tempFile)
mqc_report_file = tempFile.toString()
} else {
// Local path - just pass the path string (template will create File object)
mqc_report_file = mqc_report.toString()
}
} catch (Exception e) {
log.warn("Error accessing MultiQC report: ${e.message}")
}
}


// Check if we are only sending emails on failure
def email_address = email
if (!email && email_on_fail && !workflow.success) {
Expand All @@ -295,7 +315,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi

// Render the sendmail template
def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report_file, mqcMaxSize: max_multiqc_email_size.toBytes()]
def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
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