Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.1.0] - 2024-10-22

Changed

Updated GENCODE versions:
- Human genome updated from Release 46 to Release 47 (GRCh38.p14).
- Mouse genome updated from Release M35 to Release M36 (GRCm39).

[1.0.0] - 2024-10-03

Added

Initial Release of the Genome Reference Builder Snakemake pipeline.
Automated genome indexing for:
- Human: GENCODE Release 46 (GRCh38.p14)
- Mouse: GENCODE Release M35 (GRCm39)
Integration of essential bioinformatics tools:
- STAR (v2.7.11b)
- RSEM (v1.3.3)
- Cell Ranger (v8.0.1)
- HISAT2 (v2.2.1)
- Kallisto (v0.51.0)
- Salmon (v1.10.1)
GTF filtering step based on the 10x Genomics filtering scheme to ensure consistency between Bulk RNA-seq and Single-cell RNA-seq analyses.
Configuration file (config.yaml) pre-configured with May 2024 GENCODE versions for human and mouse genomes.
Support for both direct execution and SLURM job scheduler submission.
Comprehensive README.md with detailed instructions on installation, configuration, usage, and troubleshooting.
Project structure setup, including directories for configuration, logs, and output.