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Release 2.2.0#580

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ramprasadn merged 165 commits intomasternf-core/raredisease:masterfrom devnf-core/raredisease:devCopy head branch name to clipboardSep 13, 2024

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Commits on Jun 3, 2024

• typo

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• bump-version 2.2.0dev

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• Merge branch 'dev' into em-typo

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Commits on Jun 5, 2024

• Merge pull request #562 from nf-core/em-typo

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• adds missinf citations for bwameme

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• Merge pull request #563 from nf-core/update_docs_for_meme

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Commits on Jun 18, 2024

• change type and update container

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• Merge branch 'master' of github.com:nf-core/raredisease into patch

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Commits on Jun 20, 2024

• remove readcount interval generation

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• add to nextflow.config

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• wes updates

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• Merge pull request #571 from nf-core/modularize-everything-1

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• Merge branch 'dev' of github.com:nf-core/raredisease into modularize-everything-2

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• fix logic

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• changelog

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• update call sv workflow

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• remove skip_eklipse

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• Merge branch 'dev' of github.com:nf-core/raredisease into change-download-ci

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• add skip_smncopynumbercaller

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Commits on Jun 25, 2024

• update module

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• add skip for repeat annotation

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• update citations

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• Merge branch 'dev' of github.com:nf-core/raredisease into citations

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• changelog

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• Merge pull request #577 from nf-core/citations

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• move versions into conditionals

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• CHANGELOG

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• Merge pull request #578 from nf-core/wes_fix

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• make bcftools roh skippable for cases without affected samples

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• add warning message

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• prettier

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• Merge pull request #579 from nf-core/bcftools_roh_update

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Commits on Jul 4, 2024

• adds channels to meme mt align

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• Merge pull request #582 from nf-core/fix_mt_meme

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Commits on Jul 25, 2024

• fix: added publishDir mode in raredisease.config

  

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• Merge branch 'dev' into add_missing_publishDir_mode

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• scatter count

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• Changelog

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• Update annotate_genome_snvs.nf

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• Merge pull request #585 from nf-core/vcfanno-split

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• update module

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• add extra resource

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• update changelog

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• Merge pull request #588 from nf-core/dynamic-anno-res

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• add feature

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• Merge pull request #589 from nf-core/tabix-vcfanno

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• Corrects usage docs

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• fix lint

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• makes 0 an allowed value for sex

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• Merge pull request #595 from genomic-medicine-sweden/update_allowed_sex

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• change lane to string type

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• Merge branch 'dev' of github.com:nf-core/raredisease into update-docs

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• update usage

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• update module

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• update usage

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• Updating Sentieon DNAscope ml-model to v1.1 in test-configs

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• first attempt

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• properly remove references to bwameme in mt subworkflows

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• issue when aligner and mt_aligner has different values

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• updaet changelog

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• update cytosure conditional

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• add csi option

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• fix lint

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