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nf-core/rnadnavar: Changelog

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

1.0.0 - [2026-06-23]

Initial release of nf-core/rnadnavar.

Added

  • RNA and DNA integrated analysis pipeline for somatic mutation detection
  • Support for multiple variant callers (Mutect2, Strelka2, SAGE)
  • Comprehensive preprocessing with GATK4 best practices
  • VEP annotation and filtering capabilities
  • Consensus variant calling approach
  • RNA-specific filtering and realignment steps
  • MultiQC reporting and quality control
  • Support for both BWA-MEM and STAR alignment
  • Added support for optional Mutect2 force-calling inputs (mutect2_alleles and mutect2_alleles_tbi)
  • Added conf/empty.config to support strict-syntax-safe config loading
  • Added full pipeline nf-test (test_full.nf.test) and test snapshots
  • Added VCF simple test data for annotation testing
  • Added GitHub Actions for automated testing with nf-test
  • Added support for multiple template versions (3.2.0, 3.2.1, 3.3.1)
  • Restored rnadnavar logo in pipeline output with color support

Fixed

  • Fixed multiple strict-syntax compilation issues across local workflows and subworkflows
  • Fixed samplesheet parsing and moved tumour/normal composition validation upstream of channel creation
  • Fixed interval-preparation strict-syntax issues, including name collisions and duration handling
  • Fixed local wrappers and callers to match updated nf-core module input/output signatures and version emits
  • Fixed reference-channel consumption bugs affecting FASTA/FAI/DICT propagation in preprocessing, realignment and variant-calling paths
  • Fixed realignment-specific logic in RNA filtering and downstream consensus handling
  • Fixed MultiQC input/config channel handling and mixed software-version aggregation
  • Fixed consensus input ordering to improve deterministic behaviour when resuming runs
  • Fixed non-deterministic nf-test outputs and updated snapshots accordingly
  • Fixed includeConfig handling in nextflow.config for newer Nextflow strict syntax
  • Fixed VEP cache initialisation and updated unzip-dependent wiring
  • Fixed help text and documentation URLs
  • Fixed pipeline-specific parameter descriptions in schema
  • Fixed workflow path references and documentation links
  • Fixed consensus module caller value to avoid warnings
  • Fixed VEP cache handling and empty RNA edits processing
  • Fixed issue with run_consensus.R plotting
  • Major Fix: Resolved ConcurrentModificationException error from Java processes
  • Fixed local module implementations and configurations
  • Fixed subworkflow naming and structure issues
  • Fixed SAGE variant caller integration and configuration
  • Fixed nf-core subworkflow integrations

Changed

  • Updated the nf-core template and a broad set of nf-core modules and subworkflows
  • Harmonised FASTA/FAI/DICT channel shapes across local subworkflows
  • Updated local realignment and HISAT2 call wiring for newer module interfaces
  • Updated local samtools callers (view, convert, merge, faidx) to current nf-core module contracts
  • Updated local GATK and Picard integrations, including restored patches for picard/filtersamreads and gatk4/splitncigarreads
  • Replaced deprecated tabix usage with current htslib-based handling where appropriate
  • Updated nf-test plugin configuration and test snapshots
  • Cleaned up code formatting and style across configuration files
  • Updated test configurations and .nftignore files
  • Improved subworkflow organization and consistency
  • Massive speed up to run_consensus.R
  • Migrated consensus module from custom Docker container to Seqera Wave containers
  • Updated all nf-core modules to latest versions
  • Updated template to nf-core/tools version 3.3.1
  • Updated GitHub workflows and CI/CD configurations
  • Updated Nextflow minimum version requirement from >=23.04.0 to >=24.04.2

Removed

  • Removed obsolete tabix modules and deprecated module usage paths
  • Removed leftover config and workflow parameters no longer used after the template/module refresh (for example hook_url)
  • Cleaned up unused VCFlib and VT variant processing modules
  • Removed obsolete module configurations and test files
  • Removed redundant workflow components