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Release 2.1.0 #555

Merged
merged 108 commits into from
May 29, 2024
Merged

Release 2.1.0 #555

merged 108 commits into from
May 29, 2024

Commits on Mar 18, 2024

  1. bumpversion2.1.0dev

    @ramprasadn
    ramprasadn committed Mar 18, 2024
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  2. Merge pull request #533 from genomic-medicine-sweden/bump-version 

    Bumpversion 2.1.0dev
    @ramprasadn
    ramprasadn authored Mar 18, 2024
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  3. update changelog

    @ramprasadn
    ramprasadn committed Mar 18, 2024
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  4. Merge pull request #534 from genomic-medicine-sweden/update_changelog 

    Update changelog
    @ramprasadn
    ramprasadn authored Mar 18, 2024
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Commits on Apr 11, 2024

  1. patch

    @ramprasadn
    ramprasadn committed Apr 11, 2024
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  2. update output

    @ramprasadn
    ramprasadn committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. update me vep

    @ramprasadn
    ramprasadn committed Apr 12, 2024
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  2. remove variant consequences

    @ramprasadn
    ramprasadn committed Apr 12, 2024
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Commits on Apr 16, 2024

  1. update test config

    @ramprasadn
    ramprasadn committed Apr 16, 2024
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Commits on Apr 19, 2024

  1. fixing typo

    @jemten
    jemten committed Apr 19, 2024
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Commits on Apr 29, 2024

  1. update repeat expansion files

    @jemten
    jemten committed Apr 29, 2024
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  2. adding explicit temps

    @jemten
    jemten committed Apr 29, 2024
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  3. adds trailing comma

    @jemten
    jemten committed Apr 29, 2024
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  4. remove lane from meta

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  5. Merge pull request #541 from genomic-medicine-sweden/config_update 

    adding explicit temps
    @jemten
    jemten authored Apr 29, 2024
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  6. move hmtnote to the top in mt annotation wf

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  7. remove blank line

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  8. Merge branch 'patch' of github.com:nf-core/raredisease into patch

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  9. update pedigree file

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  10. fix error

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  11. fix versions

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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  12. update output docs

    @ramprasadn
    ramprasadn committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. fix reheader args

    @ramprasadn
    ramprasadn committed Apr 30, 2024
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  2. ignore error from bwa-mem2 and if output is missing, run bwa

    @rannick
    rannick committed Apr 30, 2024
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  3. change logical gate

    @rannick
    rannick committed Apr 30, 2024
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  4. typo

    @rannick
    rannick committed Apr 30, 2024
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  5. move vcfanno to the top of anno mt snvs workflow

    @ramprasadn
    ramprasadn committed Apr 30, 2024
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  6. change syntax

    @rannick
    rannick committed Apr 30, 2024
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  7. change logical gate

    @rannick
    rannick committed Apr 30, 2024
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  8. change logical gate

    @rannick
    rannick committed Apr 30, 2024
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Commits on May 2, 2024

  1. try a retry with more memory

    @rannick
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  2. try a retry with more memory

    @rannick
    rannick committed May 2, 2024
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  3. try a retry with more memory

    @rannick
    rannick committed May 2, 2024
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  4. change logic

    @rannick
    rannick committed May 2, 2024
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  5. change logic

    @rannick
    rannick committed May 2, 2024
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  6. change logic

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    rannick committed May 2, 2024
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Commits on May 3, 2024

  1. change if statement

    @rannick
    rannick committed May 3, 2024
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  2. change if statement

    @rannick
    rannick committed May 3, 2024
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  3. change if statement

    @rannick
    rannick committed May 3, 2024
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  4. change if statement

    @rannick
    rannick committed May 3, 2024
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  5. change if statement

    @rannick
    rannick committed May 3, 2024
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  6. add tmp channel

    @rannick
    rannick committed May 3, 2024
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Commits on May 6, 2024

  1. Include "other" variants for CADD to analyse multallelic indels

    @fa2k
    fa2k committed May 6, 2024
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  2. update align

    @ramprasadn
    ramprasadn committed May 6, 2024
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  3. Merge branch 'patch' into bwafallback

    @ramprasadn
    ramprasadn committed May 6, 2024
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  4. Describe change for #545

    @fa2k
    fa2k committed May 6, 2024
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Commits on May 7, 2024

  1. update param

    @ramprasadn
    ramprasadn committed May 7, 2024
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  2. arrange param

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Commits on May 8, 2024

  1. Template update for nf-core/tools version 2.14.0

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    nf-core-bot committed May 8, 2024
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Commits on May 9, 2024

  1. Template update for nf-core/tools version 2.14.1

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    nf-core-bot committed May 9, 2024
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Commits on May 14, 2024

  1. Merge branch 'TEMPLATE' of github.com:nf-core/raredisease into templa… 

    …te-update
    @ramprasadn
    ramprasadn committed May 14, 2024
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  2. update test one sample

    @ramprasadn
    ramprasadn committed May 14, 2024
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  3. fix lint error

    @ramprasadn
    ramprasadn committed May 14, 2024
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  4. fix lint

    @ramprasadn
    ramprasadn committed May 14, 2024
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  5. Merge pull request #548 from nf-core/template-update 

    Template update v2.14.1
    @ramprasadn
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  6. Merge remote-tracking branch 'upstream/dev' into dev

    @fa2k
    fa2k committed May 14, 2024
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  7. Merge pull request #545 from fa2k/dev 

    Include "other" variants for CADD to analyse multallelic indels
    @fa2k
    fa2k authored May 14, 2024
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Commits on May 16, 2024

  1. changed valid values for sex 

    This is now compatible with the PED file format and documentation
    @sima-r
    sima-r authored May 16, 2024
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Commits on May 17, 2024

  1. Merge branch 'dev' into patch

    @ramprasadn
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  2. update changelog

    @ramprasadn
    ramprasadn committed May 17, 2024
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  3. Merge pull request #538 from nf-core/patch 

    Refactoring + other issues with cadd and samtools merge
    @ramprasadn
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  4. Merge branch 'dev' of github.com:nf-core/raredisease into bwafallback

    @ramprasadn
    ramprasadn committed May 17, 2024
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  5. update changelog

    @ramprasadn
    ramprasadn committed May 17, 2024
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  6. refactor mito

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    ramprasadn committed May 17, 2024
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  7. updatae changelog

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    ramprasadn committed May 17, 2024
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  8. Update align_bwa_bwamem2.nf

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Commits on May 18, 2024

  1. Merge branch 'dev' into inputschemafixes

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Commits on May 19, 2024

  1. add mem and index

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    ramprasadn committed May 19, 2024
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  2. add align

    @ramprasadn
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  3. update changelog

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    ramprasadn committed May 19, 2024
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Commits on May 20, 2024

  1. Update CHANGELOG.md

    @sima-r
    sima-r authored May 20, 2024
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  2. ran prettier

    @sima-r
    sima-r authored May 20, 2024
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  3. Merge pull request #551 from nf-core/bwafallback 

    Bwafallback
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  4. Merge branch 'dev' into inputschemafixes

    @ramprasadn
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  5. Merge pull request #550 from nf-core/inputschemafixes 

    changed valid values for  the sex variable
    @sima-r
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  6. Merge branch 'dev' of github.com:nf-core/raredisease into mito_wes

    @ramprasadn
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  7. Merge pull request #552 from nf-core/mito_wes 

    Skip mitochondrial analysis for WES
    @ramprasadn
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  8. Merge branch 'dev' of github.com:nf-core/raredisease into addbwameme

    @ramprasadn
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  9. review suggestions

    @ramprasadn
    ramprasadn committed May 20, 2024
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  10. fix error

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    ramprasadn committed May 20, 2024
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Commits on May 21, 2024

  1. metromap

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  2. Merge pull request #553 from nf-core/addbwameme 

    Add bwameme
    @ramprasadn
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Commits on May 23, 2024

  1. fix

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  2. update changelog

    @ramprasadn
    ramprasadn committed May 23, 2024
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  3. Update CHANGELOG.md

    @ramprasadn
    ramprasadn authored May 23, 2024
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  4. fix error

    @ramprasadn
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  5. Merge branch 'me_required_files' of github.com:nf-core/raredisease in… 

    …to me_required_files
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  6. Merge pull request #556 from nf-core/me_required_files 

    Fix join issues in ME calling subworkflow
    @ramprasadn
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Commits on May 24, 2024

  1. resolve warnings

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  2. update qcbam subworkflow

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  3. update changelog

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  4. update modules

    @ramprasadn
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  5. Update CHANGELOG.md 

    Co-authored-by: Anders Jemt <[email protected]>
    @ramprasadn @jemten
    ramprasadn and jemten authored May 24, 2024
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  6. update modules

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  7. Merge pull request #557 from nf-core/refactor 

    Resolve warnings
    @ramprasadn
    ramprasadn authored May 24, 2024
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  8. Merge branch 'dev' of github.com:nf-core/raredisease into modules_update

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Commits on May 27, 2024

  1. updating meta.sex type check

    @jemten
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  2. switching equals to matches

    @jemten
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Commits on May 28, 2024

  1. Merge pull request #559 from nf-core/fix_gens_sex 

    updating meta.sex type check
    @jemten
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  2. Merge branch 'dev' into modules_update

    @jemten
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  3. update changelog and modules [skip ci]

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  4. update gatk

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  5. Merge pull request #558 from nf-core/modules_update 

    update modules
    @ramprasadn
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  6. refactor

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  7. Merge pull request #561 from nf-core/refactor 

    refactor
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Commits on May 29, 2024

  1. bump-version

    @ramprasadn
    ramprasadn committed May 29, 2024
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  2. Update conf/modules/align_sentieon.config 

    Co-authored-by: Felix Lenner <[email protected]>
    @ramprasadn @fellen31
    ramprasadn and fellen31 authored May 29, 2024
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  3. Update CHANGELOG.md

    @ramprasadn
    ramprasadn authored May 29, 2024
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