All notable changes to this project will be documented in this file.
- Fixed HPC profile
- Added SLURM executor throttling (queueSize, submitRateLimit) for large-scale runs.
- Added retry logic with resource scaling for OOM and timeout failures.
- Added scratch support for node-local I/O performance.
- Capped memory and CPU resources with Math.min() to prevent exceeding node limits.
- Removed redundant executor and queue declarations from process selectors.
- Updated
- Trim Galore v2 wihich is implemented in Rust and runs faster than the older v0.6.x.
- MultiQC v1.34
- Conditional execution of alelle count process.
- Added pipeline execution report.
- Initial release of nf-rna-wasp-allele-count, a Nextflow pipeline to perform allele-specific expression analysis from RNA-seq data using a WASP-aware alignment strategy.
- Implements modular Nextflow DSL2 workflow with sample-wise output organization.
- Major features:
- Genotype-aware RNA-seq alignment with STAR + WASP correction.
- Allele-specific read counting (REF/ALT) from RNA-seq BAMs.
- Reporting of depth, mapping quality, base-quality summaries, and VAF.
- Supports execution with Docker, Singularity, Apptainer, and SLURM HPC environments.