nf-core / nf-core/tools

Improving email documentation

Open
#1,956 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

With an nf-core created pipeline (via nf-core create), there is an email feature, relying on the host system having sendmail setup. Currently, the nf-core documentation seems to suggest that you can simply provide your email as a parameter (--email your.email@domain.com), and it should work out of the box. The nextflow documentation as shown here clarifies the setup requirements for this to work, but nf-core does not. The tips and tricks section of the nf-core documentation mention the email feature as:

Specify --email your@email.com to receive emails when your pipeline completes

I believe this could be changed to something like:

Specify --email your@email.com to receive emails when your pipeline completes. Note that this requires the sendmail linux service to be setup in your environment.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the tips and tricks section of the nf-core documentation and compare its email guidance with the linked Nextflow mail documentation. Update the email note to explain that the host environment must have the sendmail service configured, then verify the wording no longer implies that email works out of the box.

Written by the indexing model from the issue text.

Assessment

Tech stack
linux
Domain
documentation
Issue type
Documentation
Difficulty
1/5
Estimated time
Under an hour
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
50/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.