3.9.0 - Sarvesjåhkå

What's Changed

• Back to dev (3.9.0dev) by @FriederikeHanssen in #2139
• fix: sort final vcf in varlociraptor sbwfs and update varlociraptor by @famosab in #2055
• Add CRAM_TO_BAM to parabricks by @famosab in #2087
• Fix MuSE timestamp and change to strict syntax by @famosab in #2129
• Fix: varlociraptor collecting multiple scenario files for one sample by @famosab in #2143
• Update vcf_annotate_snpeff subworkflow by @famosab in #2141
• Add developer guidelines and CLAUDE.md by @FriederikeHanssen in #2144
• Fix missing params prefix for umi_tag in MarkDuplicates config by @FriederikeHanssen in #2152
• Replace custom Slack notifications with nf-slack plugin by @FriederikeHanssen in #2142
• Fix: fail early when --no_intervals used with joint germline HaplotypeCaller by @FriederikeHanssen in #2146
• Fix empty fastp output folder (#1437) by @FriederikeHanssen in #2147
• Fix alignment related strict syntax and lane issue by @famosab in #2117
• Fix strict syntax errors by @bentsherman in #2159
• Recover help message by @famosab in #2165
• FIX: Fix and extend stub tests by @maxulysse in #2167
• FIX: Update plugin dependencies by @maxulysse in #2170
• update MultiQC by @maxulysse in #2173
• chore(modules): sync all sentieon/* modules to nf-core/modules@7ad1622c by @nicorap in #2188
• fix(sentieon joint): preserve GroupKey size hint for progressive merging by @nicorap in #2189
• feat(annotation): replace local annotation cache subworkflows with nf-core subworkflows, add htslib to ensemblvep/vep by @maxulysse in #2194
• Updates controlfreec containers hdbdd923_0 to hde5307d_3 by @deathstar550 in #2190
• Fix controlfreec versions emission: swap to topics by @maxulysse in #2197
• animate metromap by @FriederikeHanssen in #2199
• Fix --save_output_as_bam flag by @FriederikeHanssen in #2154
• fix: update vep_version to 115.2-1 and correct loftee_path to /opt/conda/share by @maxulysse in #2196
• Run sentieon tests via a separate GHA by @maxulysse in #2203
• Prepare RC 3.9.0 by @maxulysse in #2169
• Add entry-point dots to animated metro map by @FriederikeHanssen in #2209
• Fix save_output_as_bam test: mark sentieon_dedup scenario by @maxulysse in #2217
• Downgrade controlfreec/assesssignificance to control-freec 11.6 by @FriederikeHanssen in #2219
• bump deepvariant & mergeing, fix some syntax issues by @FriederikeHanssen in #2220
• Address PR #2168 review feedback by @FriederikeHanssen in #2221
• Release 3.9.0 by @famosab in #2168

New Contributors

• @bentsherman made their first contribution in #2159
• @deathstar550 made their first contribution in #2190

Full Changelog: 3.8.1...3.9.0