stageAs FASTQC input files to avoid basename file collisions

[tgelafr-pfzr]

PR checklist

Closes #10923

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

[Copilot]

Pull request overview

This PR fixes filename collisions in the FASTQC module when multiple input files share the same basename (e.g., from different sequencing runs). It uses Nextflow's stageAs directive to place each input file in a uniquely numbered subdirectory.

Changes:

• Added stageAs: '?/*' to the FASTQC input declaration to avoid basename collisions when staging input files.

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