fix(gtffilter): add support for non-Ensembl GTF biotype attributes (#1886)

[kanishkanandhkumar]

Description of the change

This PR resolves an issue where non-Ensembl annotation files (e.g., NCBI, RefSeq, GENCODE) fail during GTF filtering because child features (exon) lack explicit gene_biotype or gene_type attributes.

Changes made:

• Updated modules/nf-core/custom/gtffilter/templates/gtffilter.py with a two-pass parsing strategy.
• Added key aliasing for biotype attribute variants (gene_biotype, gene_type, biotype, transcript_biotype, transcript_type).
• Implemented parent-to-child attribute inheritance so exons inherit gene_biotype from their parent gene/transcript entries when omitted.

Type of change

• Bug fix (non-breaking change which fixes an issue)

Checklist

• This fix addresses issue Add support for non-Ensembl annotation files #1886.
• Pipeline tested locally with default test profile (-profile test,docker).
• Tested against NCBI GTF datasets lacking exon biotype attributes.

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @kanishkanandhkumar,

It looks like this pull-request is has been made against the kanishkanandhkumar/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the kanishkanandhkumar/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[kanishkanandhkumar]

@nf-core-bot fix linting