Overview

• Added PEACH [WiGiTS]
• Added CIDER [WiGiTS]
• Added TEAL [WiGiTS]
• Switched to latest BWA-MEM2 changes via BWA-PLUS (see here)
• Updated Hartwig panel of normal for GRCh38 in SAGE

What’s Changed

• Post release bump by @scwatts in https://github.com/nf-core/oncoanalyser/pull/199
• Downgrade nf-schema to 2.2.0 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/200
• Fix integer overflow of fastp —split_by_lines value by @scwatts in https://github.com/nf-core/oncoanalyser/pull/190
• Fix REDUX TSV discovery for non-local files by @scwatts in https://github.com/nf-core/oncoanalyser/pull/201
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/oncoanalyser/pull/196
• Implement PEACH subworkflow by @scwatts in https://github.com/nf-core/oncoanalyser/pull/187
• Fix output prepared reference data directory names by @scwatts in https://github.com/nf-core/oncoanalyser/pull/205
• Prevent ORANGE running with incompatible CUPPA inputs by @scwatts in https://github.com/nf-core/oncoanalyser/pull/206
• Implement TEAL subworkflow by @scwatts, @luan-n-nguyen in https://github.com/nf-core/oncoanalyser/pull/189
• Implement CIDER subworkflow by @scwatts in https://github.com/nf-core/oncoanalyser/pull/188
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in https://github.com/nf-core/oncoanalyser/pull/204
• Apply minor fixes and updates by @scwatts, @luan-n-nguyen in https://github.com/nf-core/oncoanalyser/pull/207
• Switch to bwa-plus from bwa-mem2 by @luan-n-nguyen, @scwatts in https://github.com/nf-core/oncoanalyser/pull/210
• Fix PAVE container directive by @scwatts in https://github.com/nf-core/oncoanalyser/pull/212
• Configure RunsOn runner to use large disk by @scwatts in https://github.com/nf-core/oncoanalyser/pull/213
• Prepare release 2.1.0 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/214
• Fix targeted mode parameters by @luan-n-nguyen in https://github.com/nf-core/oncoanalyser/pull/217
• Reviewer recommendations and other adjustments by @scwatts in https://github.com/nf-core/oncoanalyser/pull/218
• Add metromap-style diagram for pipeline overview by @scwatts in https://github.com/nf-core/oncoanalyser/pull/219
• Release 2.1.0 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/215

Full Changelog: https://github.com/nf-core/oncoanalyser/compare/2.0.0…2.1.0

Overview

• Updated to the latest WiGiTS tools (fka hmftools)
• Added REDUX [WiGiTS]
• Added NEO for neoepitope calling [WiGiTS]
• Replaced SvPrep / GRIDSS / GRIPSS with ESVEE [WiGiTS]
• Removed MarkDups [WiGiTS]
• Implemented custom panel (and exome) support
• Implemented donor sample support

What’s Changed

• Post-release bump by @scwatts in https://github.com/nf-core/oncoanalyser/pull/95
• Add type to ref_data_hla_slice_bed entry in the nextflow_schema.json by @scoughlan2 in https://github.com/nf-core/oncoanalyser/pull/96
• Fixed typos by @bounlu in https://github.com/nf-core/oncoanalyser/pull/98
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/oncoanalyser/pull/103
• Fix “Markdups process marks aligner output as markdups output incorrectly” by @mvanniekerkHartwig in https://github.com/nf-core/oncoanalyser/pull/105
• Resource requirement tweaks by @mvanniekerkHartwig in https://github.com/nf-core/oncoanalyser/pull/107
• Add donor sample support by @scwatts in https://github.com/nf-core/oncoanalyser/pull/115
• Implement Neo subworkflow by @scwatts in https://github.com/nf-core/oncoanalyser/pull/116
• Add custom panel support by @scwatts in https://github.com/nf-core/oncoanalyser/pull/117
• Enhancement/cancer type parameter reporting in ORANGE by @rhassaine in https://github.com/nf-core/oncoanalyser/pull/126
• Implement WiGiTS 2.0.0 (fka WiGiTS 6.0) by @luan-n-nguyen in https://github.com/nf-core/oncoanalyser/pull/148
• Applying linting for CI by @scwatts in https://github.com/nf-core/oncoanalyser/pull/150
• Fix BamTools and ESVEE stubs by @scwatts in https://github.com/nf-core/oncoanalyser/pull/149
• Add img genome file to test_stub profile for CI by @scwatts in https://github.com/nf-core/oncoanalyser/pull/151
• Fix process.shell in nextfow.config for CI by @scwatts in https://github.com/nf-core/oncoanalyser/pull/152
• Update meta.yml, environment.yml and misc generic tools by @scwatts in https://github.com/nf-core/oncoanalyser/pull/154
• Make version collection more robust by @scwatts in https://github.com/nf-core/oncoanalyser/pull/141
• Qualify process names in subworkflows to disambigutate by @scwatts in https://github.com/nf-core/oncoanalyser/pull/155
• Apply JVM heap space modifier to new processes by @scwatts in https://github.com/nf-core/oncoanalyser/pull/156
• Update ORANGE and Neo entrypoints by @scwatts in https://github.com/nf-core/oncoanalyser/pull/157
• Move fastp arguments to modules.config by @SPPearce in https://github.com/nf-core/oncoanalyser/pull/75
• Prevent CUPPA writing into the Isofox work directory and invalidating cache by @scwatts in https://github.com/nf-core/oncoanalyser/pull/158
• Restore CUPPA RNA only mode by @scwatts in https://github.com/nf-core/oncoanalyser/pull/159
• Switch GRCh38_hmf to the new ALT masked genome by @scwatts in https://github.com/nf-core/oncoanalyser/pull/161
• Fix the prepare reference subworkflow by @scwatts in https://github.com/nf-core/oncoanalyser/pull/160
• Increase test profile memory limit to 30 GB by @scwatts in https://github.com/nf-core/oncoanalyser/pull/163
• Disallow CRAM RNA input by @scwatts in https://github.com/nf-core/oncoanalyser/pull/167
• Use the new Hartwig GRCh38 ALT masked reference genome by @scwatts in https://github.com/nf-core/oncoanalyser/pull/168
• Bump BWA to 0.7.19 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/169
• Bump linxreport to 1.1.0 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/170
• Pin VIRUSBreakend dependency RepeatMasker to 4.1.5 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/171
• Require Virus Interpreter results to run CUPPA in DNA mode by @scwatts in https://github.com/nf-core/oncoanalyser/pull/172
• Fix BAM / CRAM index discovery by @scwatts in https://github.com/nf-core/oncoanalyser/pull/173
• Fix check for existing LINX inputs by @scwatts in https://github.com/nf-core/oncoanalyser/pull/174
• Fix utilisation of user-provided BamTools directory by @scwatts in https://github.com/nf-core/oncoanalyser/pull/176
• Apply minor fixes and updates by @scwatts in https://github.com/nf-core/oncoanalyser/pull/178
• Set COBALT pcf_gamma argument when running in targeted mode by @scwatts in https://github.com/nf-core/oncoanalyser/pull/180
• Update pipeline version text displayed in the ORANGE report by @scwatts in https://github.com/nf-core/oncoanalyser/pull/179
• Update documentation by @scwatts in https://github.com/nf-core/oncoanalyser/pull/181
• Prepare release 2.0.0 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/182
• Enable loading custom pipeline config by @scwatts in https://github.com/nf-core/oncoanalyser/pull/183
• Fix the download pipeline CI/CD by @scwatts in https://github.com/nf-core/oncoanalyser/pull/185
• Release 2.0.0 by @scwatts in https://github.com/nf-core/oncoanalyser/pull/184

New Contributors

• @scoughlan2 made their first contribution in https://github.com/nf-core/oncoanalyser/pull/96
• @mvanniekerkHartwig made their first contribution in https://github.com/nf-core/oncoanalyser/pull/105
• @rhassaine made their first contribution in https://github.com/nf-core/oncoanalyser/pull/126
• @SPPearce made their first contribution in https://github.com/nf-core/oncoanalyser/pull/75

Full Changelog: https://github.com/nf-core/oncoanalyser/compare/1.0.0…2.0.0

Initial release of nf-core/oncoanalyser.