Fail to send the completion email
A pull request for this has already been merged.
- #3304 by @robsyme — merged
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
I created a new project via nf-core create (v2.14.1) and run the template pipeline with
nextflow run . -profile test,conda --outdir results --email [xxx.email.com](http://xxx.email.com/)
command on both nextflow 24.4 and 23.4 but the email cannot be delivered. I manually tuned the code and find that sendmail_html variable has length = 0, so it seems the html render engine (groovy.text.GStringTemplateEngine) has some problems behind.
def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
In the meantime, If I created the new project via nf-core v2.8 with the lib directory for addressing the email, there is no such problem.
Command used and terminal output
nextflow run . -profile test,conda --outdir results --email xxx.email.com
System information
Nextflow version: both 23.04.4 and 24.04
Hardware: HPC
Executor: local
Container engine: both conda and singularity
OS: rhel linux-8
Python version: 3.9
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the reported nf-core create project and email command, then inspect the generated assets/sendmail_template.txt and the template-rendering path that produces sendmail_html. Compare the generated output with a project created using nf-core tools v2.8; done means the completion email renders and is delivered successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100