3.7.0 - Saltoluokta

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