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nf-core/oncoanalyser: Changelog

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

[2.3.0] Spotted Nightjar - 2025-12-11

  • 268 - Apply minor fixes and updates
    • Samplesheet / version collection fixes, misc adjustments
    • Update the Hartwig panel and pipeline reference data bundles
  • 265 - Update tests and relevant GH Actions workflows / actions
    • Add full sized test data; HCC1395 (SEQC-II) tumor / normal WGS with tumor WTS
    • Enable the test profile in 'Run nf-test' GH Actions workflow and configure appropriate RunsOn instance
    • Update nf-test snapshots for each respective test
  • 267 - Update WiGiTS tools, reference data, documentation
    • Bump WiGiTS tool versions (see Software dependencies below)
    • Remove the remapping step for ALT alignments in the LILAC subworkflow
    • Update documentation, add new compute resource page
  • 247 - Improve samplesheet validation
  • 246 - Post release bump

Software dependencies

Dependency Old version New version
BamTools 1.4.2 1.5
CIDER 1.0.4 1.1
COBALT 2.1 2.2
ESVEE 1.1.2 1.2
LILAC 1.7.1 1.7.3
LINX 2.1 2.2
ORANGE 4.1 4.1.2
PAVE 1.8 1.8.2
PURPLE 4.2 4.3
REDUX 1.2 1.2.2
SAGE 4.1 4.2
TEAL 1.3.5 1.3.6
VirusInterpreter 1.7.1 1.7.2

Reference data

Name Old version New version
HMF pipeline resources 2.2.0--3 2.3.0--2
HMF TSO500 resources 2.2.0--3 2.3.0--2

[2.2.0] Royal Spoonbill - 2025-08-02

  • 241 - Apply minor fixes and updates
    • Allow 'prepare reference' feature to be driven by samplesheet
    • Set minimum stringr / stringi version for CUPPA environment
    • Reintroduce decoy sequences for ESVEE with GRCh37 genomes
    • Update WiGiTS reference data paths
    • Improve FASTQ and longitudinal sample input handling
    • Fix REDUX TSV collection in SAGE append subworkflow
    • Update CHANGELOG.md
  • 235 - Publish selected command / log files
  • 234 - Update WiGiTS tools and reference data
  • 233 - Update documentation
  • 232 - Extend the 'prepare reference' functionality
  • 231 - Implement 'purity estimate' (WISP) workflow
  • 230 - Implement 'panel resource creation' workflow
  • 220 - Add reports to tower.yml
  • 222 - Post-release bump

Software dependencies

Dependency Old version New version
AMBER 4.1.1 4.2
BamTools 1.3 1.4.2
bwa-plus 1.0.0 -
bwa-mem2 - 2.3
CHORD 2.1.0 2.1.2
COBALT 2.0 2.1
ESVEE 1.0.3 1.1.2
ISOFOX 1.7.1 1.7.2
LILAC 1.6 1.7.1
LINX 2.0.2 2.1
NEO 1.2 1.2.1
ORANGE 3.8.1 4.1
PAVE 1.7.1 1.8
PURPLE 4.1 4.2
REDUX 1.1.2 1.2
SAGE 4.0 4.1
VirusInterpreter 1.7 1.7.1
WISP - 1.2

Reference data

Name Old version New version
HMF pipeline resources 2.1.0--1 2.2.0--3
HMF TSO500 resources 2.0.0--3 2.2.0--3

Parameters

Old name New name
fastp_umi fastp_umi_enabled
redux_umi redux_umi_enabled
- purity_estimate_mode
- ref_data_types
- driver_gene_panel
- target_regions_bed
- hmftools_log_level

[2.1.0] Peruvian Pelican - 2025-06-30

  • 219 - Add metromap-style diagram for pipeline overview
  • 217 - Fix targeted mode parameters
  • 210 - Switch to bwa-plus from bwa-mem2
  • 207 - Apply minor fixes and updates
    • Update the HMF SAGE PON
    • Bump HMF pipeline resource bundles to 2.1.0--1
    • Bump LINX to 2.0.2
    • Bump PAVE to 1.7.1
    • Update CHANGELOG.md
  • 205 - Fix output prepared reference data directory names
  • 189 - Implement TEAL subworkflow
  • 188 - Implement CIDER subworkflow
  • 187 - Implement PEACH subworkflow
  • 201 - Fix REDUX TSV discovery for non-local files
  • 190 - Fix integer overflow of fastp --split_by_lines value
  • 199 - Post-release bump

[2.0.0] Flame Robin - 2025-04-10

  • 178 - Apply minor fixes and updates
    • Bump REDUX to 1.1.2
    • Bump ESVEE to 1.0.3
    • Bump ORANGE to 3.8.1
    • Update Hartwig pipeline and TSO500 panel resources
    • Restore missing fastp threads argument
    • Update CHANGELOG.md
  • 176 - Fix utilisation of user-provided BamTools directory
  • 174 - Fix check for existing LINX inputs
  • 173 - Fix BAM / CRAM index discovery on cloud platforms
  • 172 - Require Virus Interpreter results to run CUPPA in DNA mode
  • 171 - Pin VIRUSBreakend dependency RepeatMasker to 4.1.5
  • 170 - Bump linxreport to 1.1.0
  • 169 - Bump BWA to 0.7.19
  • 168 - Switch to the new Hartwig GRCh38 ALT masked reference genome
  • 167 - Disallow CRAM RNA input
  • 160 - Fix prepare reference subworkflow
  • 159 - Restore CUPPA RNA-only mode
  • 158 - Prevent CUPPA writing into the Isofox work directory, invalidating cache
  • 75 - Move fastp trimming arguments to modules.config
  • 157 - Update ORANGE and Neo entrypoints
  • 156 - Apply JVM heap space modifier to new processes
  • 155 - Qualify process names in subworkflows to disambigutate
  • 141 - Make version collection more robust
  • 154 - Update meta.yml, environment.yml and misc generic tools
  • 149 - Fix BamTools and ESVEE stubs
  • 148 - Implement WiGiTS 2.0.0 (fka WiGiTS 6.0)
  • 126 - Expose ORANGE cancer type parameter
  • 117 - Add custom panel support
  • 116 - Implement Neo subworkflow
  • 115 - Add donor sample support
  • 107 - Resource requirement tweaks
  • 105 - Adjust MarkDups outputs to improve efficiency with k8s
  • 98 - Fix typos in error messages for process and run mode check
  • 96 - Add missing type field to an entry in the nextflow_schema.json
  • 95 - Post-release bump

[1.0.0] Pied Currawong - 2024-08-26

Initial release of nf-core/oncoanalyser, created with the nf-core template.