nf-core related commands for espanso

What is nf-core?

nf-core 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.