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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,9 @@ Instructions for [nf-core pipeline](https://github.com/nf-core/proposals) approv
- One member of the core team and one member of the maintainers team.
5. [ ] Core: Verify that the pipeline name follows the [pipeline naming guidelines](/docs/guidelines/pipelines/requirements/workflow_name).
6. [ ] Core: Create a slack channel with approved pipeline name.
- [ ] Invite the Slack bot to the channel (`/invite @Full test notifications`).
This is required for CI/CD Slack notifications via the [nf-slack plugin](https://github.com/seqeralabs/nf-slack).
The bot **will silently fail** if not invited.
- [ ] Inform the new developer of the [next steps](https://nf-co.re/docs/tutorials/adding_a_pipeline/creating_a_pipeline#create-the-pipeline)
7. [ ] Core: Add the main developers to
- [ ] [#pipeline-maintainers](https://nfcore.slack.com/archives/C04QR0T3G3H)
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Expand Up @@ -80,7 +80,7 @@ To run a pipeline:

- Hyphens matter! Core Nextflow command-line options use one (`-`), whereas pipeline-specific parameters use two (`--`).
- Specify `--email your@email.com` to receive emails when your pipeline completes (requires Nextflow [mail and notification configuration](https://www.nextflow.io/docs/latest/mail.html#mail-configuration)).
- Specify `--hook_url YOUR-HOOK-URL` or set the `params.hook_url` in `nextflow.config` to receive notifications from your pipeline in Microsoft Teams or Slack. Learn how to set up an incoming webhook in [MS Teams](https://learn.microsoft.com/en-us/microsoftteams/platform/webhooks-and-connectors/how-to/add-incoming-webhook?tabs=dotnet) and in [Slack](https://api.slack.com/messaging/webhooks).
- To receive notifications from your pipeline (e.g. on completion or failure), see the [nf-slack plugin](https://github.com/seqeralabs/nf-slack) for Slack or the [nf-teams plugin](https://github.com/nvnieuwk/nf-teams) for Microsoft Teams.
- Include `-r <version-number>` to specify a release version explicitly. This guarantees the same run command will give the same results in future runs.
- Use `-resume` to restart pipelines that did not complete. This uses cached results for successful tasks from the previous run, instead of executing all tasks from scratch.
- Use `nextflow log` to find the names of all previous runs in your directory, then use `nextflow run <pipeline> -resume <run-name>` to restart a specific run.
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