Add --empty-template flag for creating modules

[mirpedrol]

Close #2091

How to run
nf-core modules create --empty-template foo

Output files:

modules/nf-core/foo/main.nf

process FOO {
    tag "$meta.id"
    label 'process_single'

    conda "YOUR-TOOL-HERE"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
        'quay.io/biocontainers/YOUR-TOOL-HERE' }"

    input:
    tuple val(meta), path(input)

    output:
    tuple val(meta), path("*"), emit: output
    path "versions.yml"           , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    """

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
    END_VERSIONS
    """
}

modules/nf-core/foo/meta.yml

name: "foo"
description: write your description here
keywords:
  - sort
tools:
  - "foo":
      description: ""
      homepage: ""
      documentation: ""
      tool_dev_url: ""
      doi: ""
      licence: ""

input:
  # Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  
  
  - input:
    type: file
    description: 
    pattern: 

output:
  #Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  
  - output:
    type: file
    description: 
    pattern: 

authors:
  - "@mirpedrol"

tests/modules/nf-core/foo/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { FOO } from '../../../../modules/nf-core/foo/main.nf'

workflow test_foo {
    
    input = [
        [ id:'test', single_end:false ], // meta map
        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
    ]

    FOO ( input )
}

tests/modules/nf-core/foo/test.yml

- name: "foo"
  command: nextflow run ./tests/modules/nf-core/foo -entry test_foo -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/foo/nextflow.config
  tags:
    - "foo"
  files:
    - path: ""

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #2175 (c6cf507) into dev (110cec8) will decrease coverage by 0.01%.
The diff coverage is 80.26%.

@@            Coverage Diff             @@
##              dev    #2175      +/-   ##
==========================================
- Coverage   71.54%   71.53%   -0.01%     
==========================================
  Files          77       77              
  Lines        8367     8340      -27     
==========================================
- Hits         5986     5966      -20     
+ Misses       2381     2374       -7     

Impacted Files	Coverage Δ
nf_core/bump_version.py	89.47% <ø> (ø)
nf_core/create.py	65.01% <ø> (+0.38%)	⬆️
nf_core/download.py	52.72% <ø> (ø)
nf_core/launch.py	63.26% <ø> (ø)
nf_core/lint/__init__.py	74.18% <ø> (ø)
nf_core/lint/files_unchanged.py	72.61% <ø> (ø)
nf_core/lint/template_strings.py	87.50% <ø> (ø)
nf_core/list.py	79.82% <ø> (ø)
nf_core/modules/bump_versions.py	63.90% <ø> (ø)
nf_core/utils.py	82.38% <ø> (+0.24%)	⬆️
... and 11 more

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[mashehu]

Nice! I am just not 100% sure about the parameter name (as usual 🙄). "minimal" is a bit too vague for me (could for example mean without tests, like we do for local modules). What do you think about --no-todos?

[mirpedrol]

🤔 There are also some things stripped apart from TODOs, like the command example. Maybe --empty-template or something similar?

[mashehu]

thinking more about this functionality, it might be cumbersome to always have to remove the todo statements, at the same time they help to be sure one doesn't forget something (which might happen easily with all the different files). Do we lint for the most important things we mention in the todos?

[mirpedrol]

Yes, I agree it's good to have them as a checklist, I think this feature is only for people who are very used to add modules and don't need them.
We don't lint for most of the TODOs because it's difficult to lint those, they depend a lot on the module. But we lint for the important things, and reviewers usually check the steps mentioned in the TODOs.