nf-core / nf-core/tools

--empty-template flag not producing fully empty module template

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

Description

Description of the bug

After executing nf-core modules create <tool_name> --empty-template TODOs are still there in main.nf.test and environment.yml. Also the meta.yml is getting generated with an older weird format for descriptions wher ethe last ] would skip to the next line.

Command used and terminal output
nf-core modules create <tool_name> --empty-template

// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
// nf-core modules test pygenprop/info
nextflow_process {

    name "Test Process PYGENPROP_INFO"
    script "../main.nf"
    process "PYGENPROP_INFO"

    tag "modules"
    tag "modules_nfcore"
    tag "pygenprop"
    tag "pygenprop/info"

    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used


input:
  - - meta:
        type: map
        description: Groovy Map containing sample information. e.g. `[ id:'sample1'
          ]`
System information

Shouldn't be required

Contributor guide

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce nf-core modules create <tool_name> --empty-template and inspect the generated main.nf.test, environment.yml, and meta.yml files. The fix is complete when the empty template contains no TODOs and the meta.yml description uses the expected formatting; verify the generated output against the reported example.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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