Add configurable attribute_type parameter for featureCounts#36
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This enhancement makes the featureCounts `-g` parameter configurable instead of being hardcoded to "gene_id". Users can now specify different attribute types (e.g., transcript_id, ID) in their config.yaml file, providing greater flexibility for different annotation formats including GFF files. Changes: - Add attribute_type parameter to config.yaml and test_config.yaml (defaults to "gene_id" for backward compatibility) - Update paired_counts.smk to use configurable attribute_type in both all and unique read counting rules - Update single_counts.smk to use configurable attribute_type in both all and unique read counting rules 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
…ow-error-on-pr Reduce CI Snakemake resource usage
…ow-error-on-pr Restore test_samples_long.csv in PR workflow runs
…on-for-qualimap Convert GFF annotations upfront with validation
Updated README to clarify usage of Singularity and testing instructions.
Clarify GFF to GTF conversion process in README.
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This enhancement makes the featureCounts
-gparameter configurable instead of being hardcoded to "gene_id". Users can now specify different attribute types (e.g., transcript_id, ID) in their config.yaml file, providing greater flexibility for different annotation formats including GFF files.Changes:
🤖 Generated with Claude Code