fix: make isoformanalyzer annotation match transcriptome reference

[dlaehnemann]

Summary by CodeRabbit

• Chores
  • Updated the annotation retrieval process in the workflow to use a new parameter and wrapper version, which may affect how annotation data is processed.

[coderabbitai]

Walkthrough

The change updates the get_annotation rule within a Snakemake workflow file. Specifically, it replaces the parameter fmt="gtf" with flavor="chr_patch_hapl_scaff" and updates the wrapper version from "0.80.1/bio/reference/ensembl-annotation" to "v6.0.1/bio/reference/ensembl-annotation". These adjustments modify the parameters provided to the wrapper and specify a new version for annotation retrieval.

Changes

File(s)	Change Summary
workflow/rules/ref.smk	Updated get_annotation rule: replaced fmt="gtf" with flavor="chr_patch_hapl_scaff" and changed wrapper version to "v6.0.1/bio/reference/ensembl-annotation"

Poem

In the warren of code, a new flavor appears,
Old formats replaced, as the wrapper steers.
With "chr_patch_hapl_scaff" now in command,
And v6.0.1 lending a helping hand.
The annotation hops forward, swift and neat—
A rabbit’s delight in a workflow so sweet!
🐇✨

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[coderabbitai]

Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between de347fa and 2758157.

📒 Files selected for processing (1)

• workflow/rules/ref.smk (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (1)

• GitHub Check: formatting

🔇 Additional comments (1)

workflow/rules/ref.smk (1)

26-26: Appropriate flavor parameter added for consistent annotation.

The addition of the flavor="chr_patch_hapl_scaff" parameter with the explanatory comment is a good change. This specifies a particular Ensembl FTP flavor that will help ensure that the annotation data matches the transcriptome reference as intended by the PR title. The chr_patch_hapl_scaff flavor includes chromosome patches, haplotype sequences, and scaffolds which provides comprehensive annotation data.