Merge pull request #219 from famosab/nf-up

nf-core: Add more commands and update links to new docs

Author: smeech

packages/nf-core/0.1.0/README.md

@@ -0,0 +1,93 @@
+# nf-core related commands for espanso
+
+## What is nf-core?
+
+[nf-core](https://nf-co.re/) is a community effort for building high-quality, reproducible bioinformatics pipelines with Nextflow.  
+It provides:
+
+- Standardized pipeline structure
+- Automated linting and CI checks
+- Consistent documentation and release practices
+- Shared best practices across many pipelines
+
+## What this espanso package is for
+
+This package adds quick text expansions for frequent nf-core comments used in:
+
+- GitHub pull request reviews
+- GitHub issues
+- Slack support and collaboration
+
+The goal is to make repeated feedback faster, clearer, and more consistent.
+
+## Trigger discovery
+
+Most triggers in this package start with `:nfc-`.
+
+Type `:nfc-` in any text field where Espanso is active (for example GitHub or Slack) to see and use the nf-core shortcuts quickly.
+
+## Available triggers
+
+This package uses grouped triggers with selection popups.
+Most groups have one descriptive trigger, with aliases only where helpful.
+
+- `:nfc-lint`
+	- Replacement:
+		- You can run `nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment` on this file to clean this up nicely.
+- `:nfc-modcore`
+	- Possible replacements:
+		- According to the module specifications we want the module name reflected in the process name.
+		- Let the module user decide output naming via `ext-prefix` and use `${prefix}`.
+		- Can you please add ontologies to the meta map?
+		- Can we put all these inputs into one tuple?
+		- If input and output names can overlap, use `task.ext.prefix` to disambiguate (example guard: `if ("${tsv}" == "${prefix}.tsv") ...`).
+- `:nfc-versions`
+	- Possible replacements:
+		- Versions expression snippet:
+			- `process.out.findAll { key, val -> key.startsWith('versions') }`
+		- Request to migrate versions output to topics.
+- `:nfc-snap` (alias: `:nfc-test`)
+	- Possible replacements:
+		- Use `snapshot(sanitizeOutput(process.out)).match()` for cleaner snapshots.
+		- Ask to include more files in snapshots.
+		- Use `snapshot(sanitizeOutput(process.out)).match()` for stub assertions.
+		- Use `nft-bam` (including `.getReadsMD5()`) for BAM content assertions.
+		- Use `nft-vcf` for VCF content assertions.
+		- Insert a GitHub ````suggestion```` block with `snapshot(sanitizeOutput(process.out)).match()`.
+		- Include `ext.args` in `main.nf.test`.
+- `:nfc-docker`
+	- Possible replacements:
+		- Encourage bringing tools to bioconda so docker/singularity containers can be built automatically.
+		- Recommend uploading custom containers to nf-core quay.io and requesting via `#request-core`.
+- `:nfc-contrib`
+	- Possible replacements:
+		- Ask contributor to join the nf-core GitHub organization so CI can run.
+		- Recommend one module per PR.
+		- Ask to split a large PR into one PR per module/subworkflow.
+- `:nfc-thanks`
+	- Possible replacements:
+		- Thank-you note with mention of added review comments.
+		- Thank-you note with guidance to module specs and examples in repository.
+- `:nfc-pipeline` (alias: `:nfc-info`)
+	- Possible replacements:
+		- Request `nextflow.log`, `samplesheet.csv`, and the exact run command.
+		- Suggest using a custom configuration file (with docs reference).
+- `:prtodo`
+	- Replacement:
+		- `-commenter:@me -review:changes-requested`
+- `:nfc-github` (alias: `:nfc-gh`)
+	- Possible replacements:
+		- Recommend opening a new PR from the latest module template via `nf-core m create`.
+		- Close due to inactivity message with reopen/new PR guidance.
+
+## Typical usage
+
+1. Type a configured trigger in GitHub or Slack.
+2. Let espanso expand it into the full comment.
+3. Adjust project-specific details before sending.
+
+## Notes
+
+- Keep expansions short, respectful, and actionable.
+- Prefer links to nf-core docs when suggesting standards.
+- Update triggers regularly as team conventions evolve.

packages/nf-core/0.1.0/package.yml

@@ -2,6 +2,6 @@ name: "nf-core"
 title: "nf-core related commands for espanso"
 description: nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. This package provides commands to interact with pull requests on nf-core repositories and in the Slack channel. If you have something to add to this package, please open a pull request on the GitHub repository.
 homepage: "https://nf-co.re/"
-version: 0.1.0
+version: 0.1.1
 author: Famke Bäuerle
 tags: ["nf-core", "nextflow", "bioinformatics", "pipelines", "slack", "github"]