Sarek 3.4.3 - Loametjåhkkå

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