Linter drops trailing double quote when parsing eval() in topics

[pinin4fjords]

Description of the bug

When linting modules that use topic: versions with eval-based version collection, the linter incorrectly drops the trailing double quote from sed/awk commands when comparing to meta.yml. This means meta.yml must have a key missing the closing " to pass lint.

Example

main.nf has:

tuple val("${task.process}"), val('ribodetector'), eval('ribodetector --version | sed "s/ribodetector //"'), emit: versions_ribodetector, topic: versions

The eval string is: ribodetector --version | sed "s/ribodetector //"

To pass lint, meta.yml must use this malformed key (missing closing "):

topics:
  versions:
    - - ${task.process}:
          type: string
          description: Name of the process
      - ribodetector:
          type: string
          description: Name of the tool
      - ribodetector --version | sed "s/ribodetector //:
          type: string
          description: Version of ribodetector used

If you write the correct key WITH the closing ":

      - ribodetector --version | sed "s/ribodetector //":

Linter fails:

correct_meta_topics: Module meta.yml does not match main.nf. Topics should contain: 
{'versions': [['${task.process}', 'ribodetector', 'ribodetector --version | sed "s/ribodetector //']]}

Note: "s/ribodetector //' - the ' is the Python string delimiter, revealing the expected content is ribodetector --version | sed "s/ribodetector // (missing trailing ").

Observed in existing modules

This pattern appears in multiple existing modules including samtools/view, fastqc, etc. - all have meta.yml with truncated eval command keys missing the trailing ".

Related

Possibly related to #3901 (--fix produces mangled output) and #3530 (incorrect parsing with special characters).

System information

• nf-core/tools: 3.5.1
• Nextflow: 24.10.0
• OS: macOS

PR where encountered

nf-core/modules#9474

[mashehu]

Should be fixed now