Template reports errors though there weren't any

[apeltzer]

[e6/f4ada4] Submitted process > multiqc
WARN: [nf-core/eager] Could not attach MultiQC report to summary email
Warning, pipeline completed, but with errored process(es)
Number of ignored errored process(es) : 0
Number of successfully ran process(es) : 2
[nf-core/eager] Pipeline completed successfully
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

This confuses users as they think something failed. Better to have an expression there to just have the warning there when something fails for real ;-)

@maxibor Can you have a look maybe?

[drpatelh]

@pditommaso We currently have this line in the template for the email notification

tools/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf

Line 370 in fabd258

if (workflow.stats.ignoredCountFmt > 0 && workflow.success) {

However, I believe the variable workflow.stats.ignoredCountFmt is a string which is why we are still getting the above output even if workflow.stats.ignoredCountFmt == 0 and workflow.success == true.

This is fixed by converting that variable to an integer:
if (workflow.stats.ignoredCountFmt.toInteger() > 0 && workflow.success) {

Im just wondering whether this is the safest way to do this because I have seen other instances in the NF repo which will most likely fail the integer conversion:
https://github.com/nextflow-io/nextflow/blob/b49e6d74dae782def6be2b087d06fdd8fa6b9291/modules/nextflow/src/test/groovy/nextflow/trace/WorkflowStatsTest.groovy#L219

[drpatelh]

if (workflow.stats.ignoredCountFmt != "0" && workflow.success) {

Also works, and avoids the integer conversion.

[maxibor]

Oups, totally missed this one in the middle of the all the other nf-core emails.
New mail filters in place since last week made it pop out again only today with @drpatelh comment ;)
I propose #338 to fix it

[pditommaso]

The stats structure is defined by this class. Therefore you should use workflow.stats.ignoredCount instead of using the fmt field.

[drpatelh]

Fixed in #337