NfcoreTemplate's email function requires multiqc_report #2272
Description
Description of the bug
The email function throws exceptions if a multiqc_report is not provided, although the function signature suggests that the parameter should be optional:
public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {For non-genomics pipelines such as microscopy, there is currently no multiqc report, so it would be nice for this parameter to be optional. Currently, if I call email like this:
NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)It produces this output:
WARN: Access to undefined parameter `max_multiqc_email_size` -- Initialise it to a default value eg. `params.max_multiqc_email_size = some_value`
ERROR ~ Failed to invoke `workflow.onComplete` event handler
-- Check script './workflows/lightsheetrecon.nf' at line: 86 or see '.nextflow.log' file for more details
And this stack trace in the .nextflow.log file:
May-03 13:39:51.827 [main] ERROR nextflow.script.WorkflowMetadata - Failed to invoke `workflow.onComplete` event handler
java.lang.NullPointerException: Cannot invoke method toBytes() on null object
»»»»at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
»»»»at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:44)
»»»»at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
»»»»at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
»»»»at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
»»»»at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
»»»»at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
»»»»at NfcoreTemplate.email(NfcoreTemplate.groovy:132)
»»»»at NfcoreTemplate.email(NfcoreTemplate.groovy:57)
»»»»at NfcoreTemplate$email$5.call(Unknown Source)
»»»»at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
»»»»at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
System information
- nf-core-tools version 2.8