Changelog

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

[1.1.0] - 2025-12-08

Automatically detects and converts FAST5 files to POD5 format if needed before basecalling.
Haplotype-specific methylation analysis workflow
- New SPLIT_BAM module to split haplotagged BAM files by haplotype (HP1, HP2, untagged)
- Optional region-based filtering using BED file (--regions_bed parameter)
- Haplotype-specific methylation calling with separate outputs for each haplotype
- Support for targeted methylation analysis on specific genomic regions

Renamed VARIANT_CALL process to VARIANT_CALL_AND_PHASING to better reflect phasing functionality
Updated METHYLATION_CALL process to accept haplotype-specific BAM inputs
Modified workflow to perform methylation calling per haplotype instead of genome-wide
Updated SUMMARY (REPORT) process to handle haplotype-specific methylation outputs (BED and bedGraph files)

Methylation calling now produces separate outputs for:
- HP1 (haplotype 1) methylation calls
- HP2 (haplotype 2) methylation calls
- Both BED and bedGraph formats per haplotype
Improved output organization with haplotype-specific subdirectories

Initial release of the nf-ont-methpro pipeline for Oxford Nanopore methylation profiling.
Implements modular Nextflow DSL2 workflow with sample-wise output organization.
Major features:
- Basecalling using Dorado
- Read alignment with minimap2
- Variant calling and haplotagging using PEPPER-Margin-DeepVariant
- Methylation calling using modkit (BED and bedGraph outputs)
- Summary reporting with MultiQC
Supports execution with Docker, Singularity, Apptainer, and SLURM HPC environments.