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Oncomplete fix #1460

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robsyme wants to merge 2 commits into from
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Oncomplete fix #1460

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c4fb145
skip_sample_count
robsyme Nov 29, 2024
4773e58
Ensure that the onComplete block doesn't hang.
robsyme Nov 29, 2024
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19 changes: 0 additions & 19 deletions assets/email_template.html
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Original file line number Diff line number Diff line change
Expand Up @@ -34,25 +34,6 @@ <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed uns
<p>The full error message was:</p>
<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
</div>
""" } else if(skip_sample_count > 0) { out << """
<div
style="
color: #856404;
background-color: #fff3cd;
border-color: #ffeeba;
padding: 15px;
margin-bottom: 20px;
border: 1px solid transparent;
border-radius: 4px;
"
>
<h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed with warnings!</h4>
<p>
The pipeline finished successfully, but samples were skipped. Please check warnings at the top of the MultiQC report.
</p>
<p></p>
</div>

""" } else { out << """
<div
style="
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7 changes: 0 additions & 7 deletions assets/email_template.txt
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Expand Up @@ -17,13 +17,6 @@ The full error message was:

${errorReport}
"""
} else if (skip_sample_count > 0) {
out << """##################################################
## nf-core/rnaseq execution completed with warnings ##
##################################################
The pipeline finished successfully, but samples were skipped.
Please check warnings at the top of the MultiQC report.
"""
} else {
out << "## nf-core/rnaseq execution completed successfully! ##"
}
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8 changes: 7 additions & 1 deletion subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
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Expand Up @@ -116,10 +116,16 @@ workflow PIPELINE_COMPLETION {
id, status -> pass_strand_check[id] = status
}

// We need to ensure that the multiqc_report is a value channel (DataflowVariable).
// Queue channels will not be available in the workflow.onComplete block.
def multiqc_reports = multiqc_report.toList()

//
// Completion email and summary
//
workflow.onComplete {
assert multiqc_reports instanceof groovyx.gpars.dataflow.DataflowVariable : "Expected a value channel (DataflowVariable) for multiqc_reports inside workflow.onComplete block."

if (email || email_on_fail) {
completionEmail(
summary_params,
Expand All @@ -128,7 +134,7 @@ workflow PIPELINE_COMPLETION {
plaintext_email,
outdir,
monochrome_logs,
multiqc_report.toList()
multiqc_reports.getVal(),
)
}

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40 changes: 19 additions & 21 deletions subworkflows/nf-core/utils_nfcore_pipeline/main.nf
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