What's Changed

• Fix bcftools concat on Strelka somatic VCFs by @FriederikeHanssen in #2128

Full Changelog: 3.8.0...3.8.1

Added

Addition of the following tools:

• VEP Condel plugin to calculate Consensus Deleteriousness scores for missense mutations
• VEP Mastermind plugin to retrieve citation counts from Mastermind Genomic Search Engine
• VEP Phenotypes plugin to retrieve overlapping phenotype information from Ensembl databases
• SnpSift annotation support using --tools snpsift with --snpsift_databases CSV configuration

Bug fixes

• Remove reindex bam from outdir
• Remove exists validation from snpeff_cache and vep_cache by @pinin4fjords in #2083
• Add default for consensus_vcfs by @FriederikeHanssen in #2095
• Fix consensus calling to include all variant callers by @FriederikeHanssen in #2096, #2109
• Fix regex patterns for dbnsfp_tbi and spliceai parameters by @FriederikeHanssen in #2113
• fix(bbsplit): handle empty reads in ext.prefix for index building by @FriederikeHanssen in #2112
• Fix FilterMutectCalls not running when starting from BAM with lane field by @FriederikeHanssen in #2124

Improvements

• Test suite by @maxulysse in #2080, #2084, #2104, #2105, #2106
• Starting workflow output by @maxulysse in #2098
• Add topics for versions by @maxulysse in #2126
• Update VEP version to 115.0-0 by @FriederikeHanssen in #2119

New Contributors

• @pinin4fjords made their first contribution in #2083

Full Changelog: 3.7.1...3.8.0

What's Changed

• Fix Haplotypecaller failure on 3.7.0 in #2069
• Update modules: MultiQC (1.31 -> 1.33; adds BBsplit reporting) and BBSplit (bug on shared file systems)in #2073
• Validate umi_read_structure in #2071

Full Changelog: 3.7.0...3.7.1

What's Changed

New Tools

• #2044 - Added VCF filtering with bcftools after variant calling
• #2049 - Added consensus calling for small variants called by multiple tools (default: 2+ tools)

New Parameters:

• --filter_vcfs - Enable VCF filtering
• --bcftools_filter_criteria - Filter criteria for bcftools
• --snv_consensus_calling - Enable consensus calling
• --consensus_min_count - Minimum tool count for consensus

Bug Fixes:

• #2045 - Fixed fastp shard naming propagation through BBSplit for unique Markduplicates naming
• #2060 - Fixed bbsplit index staging by switching to symlinks instead of full copy

Developer Changes:

• #1979 - Updated prepare_genome subworkflow for language server compliance
• #2043 - Refactored postvariantcalling and separated varlociraptor
• #2053 - Fixed yte input channel to disambiguate scenario file rendering
• #2054 - Fixed typo on tbi_sentieon_dnascope channel
• #2058 - Template update for nf-core/tools v3.5.1
• #2047 - use new runsOn syntax for larger runners
• #2048 - No null value for {snpeff,vep}_cache by default
• #2058 - Important! Template update for nf-core/tools v3.5.1 by @nf-core-bot

New Contributors

• @mashehu made their first contribution in #2047

Full Changelog: 3.6.1...3.7.0

What's Changed

This release contains a fix for --aligner parabricks to use the correct intervals channel when running with --wes or --intervals <file> see #2029.

This patch release includes a bump to Nextflow 25.04.8.

Full Changelog: 3.6.0...3.6.1

What's Changed

Main new features

🧬 Lots of improvements around UMI support (#1937, @SPPearce)
⏩ Parabricks support (#1804, @famosab)
🔍 Muse (#1744, @famosab) and Sentieon TNScope (#1934, @SPPearce)
📜 MSISensor2 (#1965, @maxulysse)
🦖 Varlociraptor (#1940, @famosab)
◀️ Normalization of variants (#1770, @Patricie34 & @maxulysse)
🖖 bbsplit (#1983, @apsteinberg, @tobsecret & @FriederikeHanssen)

Changed

• Version updates:
  • VEP cache updated to v115.2
  • SnpEff updated to v5.3.0a (SnpEff cache downgraded to 99 since 105 is not available at the moment)
  • GATK4 to 4.6.1.0
  • DeepVariant to 1.9.0
  • Freebayes to 1.3.10 with QUAL filtering
• Workflow improvements:
  • Enhanced metro map
  • Doubled default process time
  • Improved sample validation
• Complete test migration:
  • All pytest tests migrated to nf-test framework for better testing infrastructure

Fixed

• Input validation: Better samplesheet validation in #1842 by @nvnieuwk and #1858 by @kjellinjonas and bugfix addReadgroupToMeta in #1849 by @thiago-miller
• CNVkit compatibility: Fixed --no_intervals usage and CPU allocation in #1928 by @SPPearce
• DeepVariant configuration: Added --sample_name argument when meta.sample available in #1992 by @matthdsm

New Parameters

• --freebayes_filter
• --msisensor2_models
• --sentieon_consensus
• --umi_base_skip
• --umi_in_read_header
• --umi_length
• --umi_location
• --umi_tag
• --varlociraptor_chunk_size
• --varlociraptor_scenario_germline
• --varlociraptor_scenario_somatic
• --varlociraptor_scenario_tumor_only

Full Changelog: 3.5.1...3.6.0

What's Changed

Changed

• Bump schema version to 2.2.1 in #1767 by @FriederikeHanssen
• Merge intervals for WES in GATK GenomicsDBImport in #1777 by @tdanhorn

Fixed

• Use file-path-pattern over file-path to hanlde glob for known_indels and known_indels_tbi to fix #1785 in #1797 by @maxulysse
• Update GHA for full_test tests in #1802 by @maxulysse

Full Changelog: 3.5.0...3.5.1

What's Changed

Added

• Tool: Lofreq callparallel by @AitorPeseta and @nevinwu in #1620, #1653, #1752
• Tool: Indexcov by @lindenb in #1613, #1752
• Expose fastp parameter --length_required by @LouisLeNezet in #1660
• Variant Calling tutorial pages to Usage section by @lescai in #1706
• Pipeline level tests by @maxulysse in #1661
• Check if flowcell id matches for paired samples by @pmoris in #1664
• Documentation on how to use WES ASCAT with chr prefixed bed file by @alexanderchang1 in #1638

Changed

• Template update for nf-core/tools v3.0.0, v3.0.1, v3.0.2 by @nf-core-bot in #1680, #1681, #1686
• Update CI actions by @maxulysse in #1657
• Migrate to nf-test by @maxulysse in #1678, #1708, #1731, #1711
• Add nf-test sharding CI by @edmundmiller in #1668
• style: Enable harshilAlignment in VS Code workspace by @edmundmiller in #1730
• Print warnings if flowcell ID cannot be retrieved instead of erroring for Nextflow <24.08.0-edge by @maxulysse in #1673
• Clean up schema file and unhid almost all parameters by @FriederikeHanssen in #1707
• Don't convert input bam files that are supplied in post-alignment steps by @FriederikeHanssen in #1728
• Update all modules by @maxulysse in #1695, #1692, #1663

Fixed

• Fix: template_version_comment GHA by @mirpedrol in #1684
• Fix: flowcell access by @FriederikeHanssen in #1693
• Fix: manifest DOI display on CLI by @maxulysse in #1694
• Fix: nf-schema tests that were not failing on lenient mode by @maxulysse in #1702
• Fix: Missing import statements on error messages(#1566) by @pharmlovex in #1712
• Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling by @bounlu in #1624
• Fix: Add missing spring and ubam files to overview pictures by @FriederikeHanssen in #1734
• Fix: add setup java 17 by @maxulysse in #1743
• Fix: bug where workflow can hang if the email parameter is set. by @robsyme in #1745
• Fix: Sentieon and add docs by @FriederikeHanssen and @edmundmiller in #1746, #1579
• Fix: Update variant calling tool - data type table in docs by @famosab in #1635
• Fix: test string by @FriederikeHanssen in #1754

Removed

• Retire snpeff_genome by @asp8200 in #1656
• Remove Strelka tumor-only somatic variant calling by @nevinwu in #1709
• Remove defaults channel from nf-core conda environments by @maxulysse in #1663
• Remove defaults channel from local modules by @FriederikeHanssen in #1755

New Contributors

• @AitorPeseta made their first contribution in #1620
• @LouisLeNezet made their first contribution in #1660
• @nevinwu made their first contribution in #1653
• @pharmlovex made their first contribution in #1712
• @pmoris made their first contribution in #1664
• @bounlu made their first contribution in #1624
• @alexanderchang1 made their first contribution in #1638
• @lindenb made their first contribution in #1613

Full Changelog: 3.4.4...3.5.0

What's Changed

• FIX: misleading docs - xref 1621 by @maxulysse in #1623
• Correct tower snpeff by @cmatKhan in #1627
• Allow dbsnp if null in germline variant calling by @cmatKhan in #1628

New Contributors

• @cmatKhan made their first contribution in #1627

Full Changelog: 3.4.3...3.4.4

What's Changed

Added

• Add support for fastq.gz.spring-files as input by @asp8200 in #1534, #1573
• Add a specific cnvkit/call module to perform calling from cns files by @lescai in #1502
• Adds the cnvkit/export module, to export called CNVs into VCF by @lescai in #1502

Changed

• Template update for nf-core/tools v2.14.1
• Unify handling of params.cnvkit_reference uniform across the three subworkflows (germline, tumour only, tumour-normal) by @lescai in #1502
• Simplify logic in args management by @maxulysse in #1521
• Update vep cache version to 111 by @maxulysse in #1557
• Cleanup + update modules by @maxulysse in #1545
• Updating documentation by @asp8200 in #1556 and by @maxulysse in #1570

Fixed

• FIX: mapped bam and bai published in the same folder by @asp8200 in #1541
• FIX: typo (strelka2 -> strelka) by @maxulysse in #1536
• FIX: Typo build_from_index -> build_only_index by @maxulysse in #1547
• FIX: Correct vep_cache_path_full when refseq/merged option is present by @YeHW in #1563
• Remove snapshot from Haplotypecaller tests by @maxulysse in #1596
• Remove snapshot from Deepvariant tests by @maxulysse in #1597
• Remove empty outdirs by @FriederikeHanssen in #1612
• Remove legacy configs of CUSTOM_DUMPSOFTWAREVERSIONS by @asp8200 in #1542

New Contributors

• @famosab made their first contribution in #1527
• @YeHW made their first contribution in #1563

Full Changelog: 3.4.2...3.4.3