nf-core
--email flag broken for v3.10.1
Description of the bug
Hello,
Am currently running nf-core/rnaseq v3.10.1 and failing to generate the completion summary email. The workflow runs to completion without any other error, however email is not sent and I get this error to stdout:
Failed to invoke `workflow.onComplete` event handler
-- Check script '/home/ubuntu/nfcoreWorkshopTesting/rnaseq/./workflows/rnaseq.nf' at line: 858 or see '.nextflow.log' file for more details
Command used and terminal output
nextflow run main.nf \
--input samplesheet.csv \
--outdir results \
--max_memory '6.GB' --max_cpus 2 \
--gtf $materials/mm10.gtf \
--fasta $materials/mm10.fa \
--star_index $materials/STAR \
--email [email protected] \
-profile singularity \
-with-report execution_report_emailTest.html \
-with-trace execution_trace_emailTest.txt \
-with-timeline timeline_emailTest.html \
-with-dag dag_emailTest.png
Relevant files
System information
- nextflow version 22.04.3.5703
- hardware: Pawsey Nimbus cloud
- executor: local
- container engine: Singularity
- OS: Linux
- nf-core/rnaseq version: 3.10.1
I was able to get past this error by installing mail on the VM (same image as @georgiesamaha) however despite no error, the email was not delivered. Outgoing email using the mail command does work, as does outgoing email on complete when using nf-core launch
Yep, it's been a pain trying to test this on my end because sendmail is really difficult to configure. We need to re-write the entire email functionality in nf-core pipelines in general to use Nextflow native options. Any contributions to a fix would be more than welcome 🙏🏽
This is usually due to misconfiguration of host email services. Happy to take a look if someone shows that this is caused by something specific to the workflow, but closing now.
