Template update for nf-core/tools version 3.5.2

[lyh970817]

Summary

• Manually sync the nf-core/gwas template from nf-core/tools 3.5.1 to 3.5.2 because the automatic template PR was not triggered for this repository.
• Update template metadata and generated docs, including .nf-core.yml, the README template badge/placeholder cleanup, and ro-crate-metadata.json.
• Apply the template cleanup from 3.5.2, including the MultiQC environment YAML header and removal of obsolete tags.yml test metadata files.

Verification

• pre-commit run --all-files
• nf-core pipelines lint (230 passed, 0 failed, 45 warnings, 2 ignored)

Notes

• This keeps the existing gwas-specific workflow logic and test input configuration intact while taking the template-side updates from 3.5.2.

[FernandoDuarteF]

Amazing. Thanks @lyh970817.

Everything looks good.

I think we can merge this.