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Release 0.4.0#514

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fellen31 merged 117 commits intomastergenomic-medicine-sweden/nallo:masterfrom devgenomic-medicine-sweden/nallo:devCopy head branch name to clipboardJan 15, 2025

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Commits on Aug 30, 2024

• Bump version to 0.4.0dev

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• Merge pull request #344 from fellen31/bump-version

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• Add metro map

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• Merge pull request #345 from fellen31/add-metro-map

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• Merge pull request #345 from fellen31/add-metro-map

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Commits on Sep 2, 2024

• Merge pull request #346 from fellen31/test-sv-calling

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Commits on Sep 3, 2024

• Change SV multisample merging to allow for other callers

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• Delete modules/nf-core/bcftools/reheader/bcftools-reheader.diff

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Commits on Sep 6, 2024

• Update paraphase to compress and index VCFs within the module

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• Change SV multisample merging to allow for other callers

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• Merge pull request #355 from fellen31/fix-paraphase

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• Remove filter_vep, add missing SNV section and PED file information to output docs

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• Merge branch 'dev' into replace-sniffles-multisample

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• Fix VEP sha in modules.json

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• Merge pull request #356 from fellen31/remove-filter-vep-from-docs

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• Merge pull request #351 from fellen31/replace-sniffles-multisample

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Commits on Sep 10, 2024

• Remove fastq QC concatenation (#352)

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Commits on Sep 11, 2024

• Merge branch 'master' into patch-merge

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• Merge pull request #360 from genomic-medicine-sweden/patch-merge

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• Add Zenodo link (#363)

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Commits on Sep 12, 2024

• Add CI test profiles to nf-test, and only use nf-test for CI (#365)

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• Sort inputs when creating PED-files, so the output it always the same (#366)

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Commits on Sep 17, 2024

• Add Severus as the default SV caller (#367)

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• Add found_in tag (#371)

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• Sort output SNVs (#370)

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Commits on Sep 18, 2024

• Remove VEP plugins from test-data (#379)

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Commits on Sep 19, 2024

• Fix untar VEP cache (#381)

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Commits on Sep 20, 2024

• Update schema and docs (#382)

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Commits on Sep 23, 2024

• Fixed, added and updated minimap2 presets (#393)

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• Patch to dev, pin dev version test-data (#397)

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Commits on Sep 25, 2024

• Add longphase (#388)

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Commits on Oct 1, 2024

• Sample names present twice in HiFiCNV output filenames (#402)

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• Test changed since without sharding (#404)

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Commits on Oct 4, 2024

• Update usage.md (#407)

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Commits on Oct 7, 2024

• Add found in tag to CNV-calling (#403)

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• [Issue #406] Updated genmod to 3.8.3 (#410)

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• [Issue #409] Updated longphase (#411)

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Commits on Oct 8, 2024

• [Issue #377] Removed bcftools/index (#412)

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• Updated Whatshap to 2.3 (#416)

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• Add found_in tag to SV-calling (#417)

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Commits on Oct 10, 2024

• Template update for nf-core/tools v3.0.1 (#422)

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Commits on Oct 11, 2024

• Issue 348 (#419)

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Commits on Oct 14, 2024

• Annotate SVs (#408)

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• Update metro map (#423)

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Commits on Oct 15, 2024

• Added --no-RG argument to minimap2 (#427)

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Commits on Oct 16, 2024

• Replace bcftools with SVDB for SV merging (#428)

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Commits on Oct 17, 2024

• Create build-docs.yml (#430)

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• Add additional mkdocs files (#431)

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Commits on Oct 18, 2024

• Fix and make docs pretty (#433)

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Commits on Oct 22, 2024

• Update SVDB and fix CALL_SVS tests (#434)

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Commits on Oct 24, 2024

• Implement nf-test for rank variants (#435)

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• Update hifiasm to 0.20 (#440)

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Commits on Oct 25, 2024

• Clean up pipeline tests (#438)

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• Run 8 parallel alignment processes by default (#418)

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Commits on Oct 29, 2024

• Merge CNV and SV calls (#429)

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Commits on Oct 30, 2024

• minimap2 preset for pacbio should be map-hifi (#441)

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• Update genmod to fix models (#444)

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• Add found_in tag to call repeat expansions (#445)

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• Rank SVs (#450)

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• Add deepvariant_vcfstatsreport (#446)

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• Refactor reference channels (#443)

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Commits on Nov 1, 2024

• Fix reference channels (#474)

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• Fix rank SVs (#479)

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Commits on Nov 4, 2024

• Update metro map (#484)

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Commits on Nov 5, 2024

• nf-test with changed-since (#487)

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• Run modkit once + general changes to methylation subworkflow (#451)

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• Fix rank SVs with multiple families (#480)

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Commits on Nov 6, 2024

• Template merge 3.0.2 (#489)

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• Update nf-core modules (#486)

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• Add keep a changelog enforcer (#491)

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• missing changelog items (#490)

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Commits on Nov 7, 2024

• Annotate repeats per family (#485)

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Commits on Nov 11, 2024

• Remove nested ifs in nallo.nf (#493)

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Commits on Nov 15, 2024

• Fix CI not passing after merge (#498)

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Commits on Nov 18, 2024

• Annotate and rank SNVs per family (#502)

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• Rename input file parameters (#488)

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Commits on Nov 19, 2024

• Filter SNVs, INDELs, CNVs and SVs (#496)

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• Update docs (#506)

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Commits on Nov 20, 2024

• Set ch_hgnc_ids default value (#507)

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• Update output.md (#509)

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Commits on Nov 22, 2024

• Fix broken link in README.md (#513)

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• Change missed single_sample and multi_sample output directories (#512)

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• Dynamically build methods description from ch_versions (#510)

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• Prep release 0.4.0 (#511)

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• Merge branch 'master' into dev

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• remove merge markers

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• prettier

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• remove merge markers in changelog

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• bump minimum master CI nextflow version to 24.04.2

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• fix tests merge mistakes and snapshot version bump

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• fix merge mistake, keeping main.nf.test

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Commits on Dec 10, 2024

• Trgt 1.2.0 (#505)

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Commits on Jan 7, 2025

• Update CHANGELOG because of reviewer comments

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Commits on Jan 8, 2025

• Update conf/modules/annotate_svs.config

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• Update conf/modules/genome_assembly.config

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• Update conf/modules/genome_assembly.config

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• Update conf/modules/rank_variants.config

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• Update conf/modules/rank_variants.config

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• Update conf/modules/rank_variants.config

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• Update conf/modules/snv_annotation.config

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• Update conf/modules/snv_annotation.config

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• Update conf/modules/snv_annotation.config

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• Update modules/local/add_found_in_tag/main.nf

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• Update subworkflows/local/utils_nfcore_nallo_pipeline/main.nf

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• Update CHANGELOG

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• Update README with clearer descriptions

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Commits on Jan 13, 2025

• rename metas to sample_metas for more descriptive naming

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• Add .collect() to allow filtering more than one family per run. (#523)

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Commits on Jan 15, 2025

• Trigger CI

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• Correct year

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