fix: gffread issue with reading gff files, writing fasta files

[nikostr]

The gffread wrapper raises ValueError: Unknown annotation format for gff files. In addition to this, the wrapper assumes that any fasta output contains the spliced exons of each transcript (produced by -w), and not e.g. spliced coding sequences or protein fasta sequences. This PR fixes both of these issues.

Unfortunately it also introduces a breaking change to how fasta files are produced. I think defaulting to -w output for fasta files is a bad solution, but could implement this if it's required.

QC

• [x] I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• [x] test.py was updated to call any added or updated example rules in a Snakefile
• [x] input: and output: file paths in the rules can be chosen arbitrarily
• [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• [x] the meta.yaml contains a link to the documentation of the respective tool or command under url:
• [x] conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features

  • Introduced a new testing rule for GFF3 files, enhancing compatibility with multiple annotation formats.
  • Added a new GFF3 annotation file defining genomic features for two manually created genes.
  • Expanded test coverage to include validation for GFF and GTF formats.

• Bug Fixes

  • Improved input validation and error handling for various annotation file formats.

• Documentation

  • Updated test functions to reflect new naming conventions and added tests for additional bioinformatics tools.

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📥 Commits

Files that changed from the base of the PR and between 732241540868701e32ed639994eef56c755f3188 and 42065bc166e3c8feb5c18fa65b53f5c40012c2f7.

📝 Walkthrough

📝 Walkthrough

📝 Walkthrough

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces modifications to the bioinformatics pipeline's handling of GFF and GTF files. It renames the existing rule test_gffread to test_gffread_gtf, adds a new rule test_gffread_gff for GFF3 files, and updates the associated input files and parameters. A new GFF3 annotation file is created, and the wrapper script is enhanced to support multiple annotation formats. Additionally, the test suite is expanded with new functions to validate these changes, improving coverage for bioinformatics tools.

Changes

File	Change Summary
bio/gffread/test/Snakefile	- Renamed rule test_gffread to test_gffread_gtf. - Added new rule test_gffread_gff for GFF3 files. Updated input files and parameters for both rules.
bio/gffread/test/annotation.gff3	- Introduced a new GFF3 file defining genomic features for two genes with transcripts, exons, and CDS.
bio/gffread/wrapper.py	- Expanded annotation format checks to include .gff and .gff3. - Updated output flag handling and added validation for fasta output flags.
test.py	- Renamed test function test_gffread to test_gffread_gtf. - Added new test function test_gffread_gff.
bio/gffread/meta.yaml	- Added fasta_flag and extra parameters in params section. Updated notes on format detection.

Possibly related PRs

• #3367: This PR directly relates to the main PR as it also modifies the Snakefile by renaming the rule test_gffread to test_gffread_gtf and introduces a new rule test_gffread_gff, aligning with the changes made in the main PR.

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[fgvieira]

Looks good. Can you just update the meta.yaml file? thanks,

[nikostr]

I ended up renaming the parameter to fasta_flag instead of out_flag. I thought this was a better description, I hope you don't mind.