Make multiqc_report optional when emailing #2273
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Nice, but I feel like you're changing more here than you need to. The try/catch block and default function arguments make me think that this was written to tolerate a missing MultiQC report already. Then at some point the type casting stuff was added and that broke.
I think that all we need to change is the params.containsKey('max_multiqc_email_size') condition and it should all work?
| @@ -128,8 +130,12 @@ class NfcoreTemplate { | |||
| def email_html = html_template.toString() | |||
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| // Render the sendmail template | |||
| def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit | |||
| def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] | |||
| def max_multiqc_email_size = params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size as nextflow.util.MemoryUnit : 0 | |||
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Or just move this into the new if block and assume it exists?
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Looking at #2272 I think that this line is basically the only one that needs to be fixed, the rest should probably already be tolerant to the report not being there (and look to me like they've been written with that in mind).
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Very insightful! I've corrected the fix along these lines.
Codecov Report
@@ Coverage Diff @@
## dev #2273 +/- ##
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Coverage 73.12% 73.12%
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Files 77 77
Lines 8432 8432
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Hits 6166 6166
Misses 2266 2266 |
This PR addresses #2272 to make multiqc_report optional during the email step. This is useful for non-genomics pipelines that do not have multiqc support currently.
It looks likely that this fix will also address #1399 but I haven't tested that.
PR checklist
CHANGELOG.mdis updateddocsis updated