demultiplex Reached automation hook

Description of the bug

Once the pipeline finishes and some email is set, it will not finish sending it. Attached the logfile of whats going on in the background, doesnt matter if i keep the hook_url set or not / once I add email functionality / use the email feature, it hangs up until I cancel.

Command used and terminal output

No response

Relevant files

No response

System information

No response

Sep 17 '24 07:09 apeltzer

Could be something around emailing functionality and the way its generated (attaching multiqc report).

Sep 17 '24 07:09 apeltzer

https://community.seqera.io/t/reached-automation-hook-nextflow-doesnt-move-on/

Sep 24 '24 14:09 apeltzer

Is this specific to the multiplex pipeline, or should this go into tools?

Oct 22 '24 07:10 grst

I am not sure, didnt try it with other pipelines

Oct 22 '24 07:10 apeltzer

This is a bug that @robsyme now fixed - see slack conversation on this with help from @FelixKrueger https://nfcore.slack.com/archives/CE5LG7WMB/p1732919344822769

Dec 03 '24 14:12 apeltzer

Fix found here https://github.com/nf-core/rnaseq/pull/1460/commits/4773e580a971e83e3368f63b1666f0d0d167f792 @nschcolnicov

Dec 03 '24 14:12 apeltzer

@apeltzer Those changes alone listed in the commit you shared didn't fix the issue for me, I'll look into it

Dec 03 '24 15:12 nschcolnicov

@apeltzer Nevermind it was my environment that was missing the mail command, PR is open for this: https://github.com/nf-core/demultiplex/pull/294

Dec 03 '24 15:12 nschcolnicov