Fix naming of GFFREAD outputs leading to null.gtf

[milos7250]

Hi all,

after the latest update to GFFREAD, they are using the id variable from the meta argument as the name of the output file. At the moment, the meta variable in this step is empty, therefore the resulting file has name null.gtf. This PR resolves this issue by specifying the basename of the input gff file as the id for this process.

PR checklist

• This comment contains a description of changes (with reason).
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• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

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[maxulysse]

yes please