3.11.0 - Guhkesvákkjåhkå

What's Changed

• back to dev (3.10.1dev) by @FriederikeHanssen in #2271
• Remove executor dependency from accelerator directive by @pditommaso in #2181
• Add parabricks/applybqsr by @famosab in #2268
• Important! Template update for nf-core/tools v4.1.0 by @nf-core-bot in #2272
• Add manifest.diagram to nextflow.config by @ewels in #2284
• Fix parabricks aligner producing nothing with --no_intervals by @FriederikeHanssen in #2275
• Wire up gVCF output for Parabricks HaplotypeCaller by @gburnett-nvidia in #2282
• Add Parabricks (GPU-based) DeepVariant by @gburnett-nvidia in #2177
• Fix relative links in output documentation by @mashehu in #2298
• Switch fix-linting to the hardened nf-core/actions reusable workflow by @mashehu in #2304
• Move seqeralabs/action-tower-launch to @v2 (v2.4.0) by @mashehu in #2306
• build: use GATK Lite containers by @adamrtalbot in #2296
• Varlociraptor: fix scenario parsing by @famosab in #2300
• Fix PARABRICKS_FQ2BAM running BQSR without indexed known-sites VCFs by @famosab in #2310
• Fix parabricks/applybqsr input tuple by @famosab in #2312
• Load nf-schema plugin in AWS full-size test config by @FriederikeHanssen in #2316
• Improve docs on nonhuman genome by @famosab in #2314
• Improve docs on Post Variantcalling by @famosab in #2317
• chore(ci): migrate AWS tests to Seqera launch rc.2 by @edmundmiller in #2321
• Use nf-core bam_applybqsr subworkflow for GATK recalibration by @maxulysse in #2318
• Prepare release 3.11.0 by @famosab in #2315
• Revise ASCAT resource generation instructions by @CharlesARoy in #2135
• Update ensemblvep modules to fix conda environment solving by @maxulysse in #2329
• Add ascat penalty by @petanska in #2328
• Update varlociraptor to 8.12.0, add --atomic-candidate-variants flag by @famosab in #2332
• Fix: pass markduplicates_pixel_distance to GATK4SPARK_MARKDUPLICATES by @jaredfischbach in #2335
• Fix/deepsomatic upstream by @FriederikeHanssen in #2337
• Add DeepSomatic somatic variant calling by @FriederikeHanssen in #2293
• Correct interval variable in BCFtools mpileup output prefix by @jaredfischbach in #2338
• Improve parabricks docs by @famosab in #2342
• fix: fail early for germline Parabricks callers without normal samples by @maxulysse in #2343
• docs: colour DeepSomatic as green dot in subway map by @maxulysse in #2344
• Release 3.11.0 by @famosab in #2313

New Contributors

• @pditommaso made their first contribution in #2181
• @ewels made their first contribution in #2284
• @CharlesARoy made their first contribution in #2135
• @petanska made their first contribution in #2328
• @jaredfischbach made their first contribution in #2335

Full Changelog: 3.10.0...3.11.0