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Release 3.0.0 - three kings #181

Merged
merged 144 commits into from
Nov 18, 2024
Merged

Release 3.0.0 - three kings #181

merged 144 commits into from
Nov 18, 2024

Commits on Jul 30, 2024

  1. feat add make database

    Lucpen committed Jul 30, 2024
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  2. fix linting

    Lucpen committed Jul 30, 2024
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Commits on Aug 20, 2024

  1. Merge branch 'dev' into drop_db

    @Jakob37
    Jakob37 committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. Merge branch 'dev' into drop_db

    @Lucpen
    Lucpen authored Aug 21, 2024
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  2. Prevent module skipping if no annotation or counts provided

    Lucpen committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. Merge branch 'drop_db' of https://github.com/genomic-medicine-sweden/… 

    …tomte into drop_db
    @Jakob37
    Jakob37 committed Aug 22, 2024
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Commits on Aug 23, 2024

  1. Merge branch 'dev' into drop_db

    @Lucpen
    Lucpen authored Aug 23, 2024
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  2. Merge branch 'dev' into drop_db

    @Lucpen
    Lucpen authored Aug 23, 2024
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Commits on Aug 27, 2024

  1. Merge branch 'dev' into drop_db

    @Lucpen
    Lucpen authored Aug 27, 2024
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Commits on Aug 28, 2024

  1. Merge pull request #158 from genomic-medicine-sweden/master 

    Merge pull request #157 from genomic-medicine-sweden/dev
    @Lucpen
    Lucpen authored Aug 28, 2024
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  2. Merge branch 'dev' into drop_db

    @Lucpen
    Lucpen authored Aug 28, 2024
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Commits on Aug 30, 2024

  1. update DROP and fix drop_config

    Lucpen committed Aug 30, 2024
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Commits on Sep 3, 2024

  1. update vep

    Lucpen committed Sep 3, 2024
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  2. update gencode version to 46

    Lucpen committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. CHANGELOG

    Lucpen committed Sep 4, 2024
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  2. Merge pull request #159 from genomic-medicine-sweden/update_reference… 

    …s_and_vep

Update vep to 112 and references encode 46
    @Lucpen
    Lucpen authored Sep 4, 2024
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  3. Merge branch 'dev' into drop_db

    @Lucpen
    Lucpen authored Sep 4, 2024
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  4. fix CHANGELOG

    Lucpen committed Sep 4, 2024
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  5. fix CHANGELOG

    Lucpen committed Sep 4, 2024
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  6. run prettier

    Lucpen committed Sep 4, 2024
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  7. update clinvar version

    Lucpen committed Sep 4, 2024
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Commits on Sep 17, 2024

  1. add count mode and overlap to sampan

    Lucpen committed Sep 17, 2024
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Commits on Sep 23, 2024

  1. Update conf/base.config

    @Lucpen
    Lucpen authored Sep 23, 2024
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Commits on Sep 24, 2024

  1. Lund updates to the drop_db branch

    @Jakob37
    Jakob37 committed Sep 24, 2024
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Commits on Oct 7, 2024

  1. Correct ignoring of exported counts

    @Jakob37
    Jakob37 committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. mkdir -p

    @Jakob37
    Jakob37 committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Update modules/local/drop_config_runAE.nf

    @Lucpen
    Lucpen authored Oct 9, 2024
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  2. Update modules/local/drop_config_runAS.nf

    @Lucpen
    Lucpen authored Oct 9, 2024
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  3. Update modules/local/drop_config_runAE.nf

    @Lucpen
    Lucpen authored Oct 9, 2024
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  4. Update modules/local/drop_config_runAE.nf

    @Lucpen
    Lucpen authored Oct 9, 2024
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Commits on Oct 10, 2024

  1. fix .nf-core.yml

    Lucpen committed Oct 10, 2024
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  2. Apply suggestions from code review 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Oct 10, 2024
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  3. apply reviewers suggestion

    Lucpen committed Oct 10, 2024
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  4. apply reviewers suggestion

    Lucpen committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Annick Renevey <[email protected]>
    @Lucpen @rannick
    Lucpen and rannick authored Oct 11, 2024
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  2. Merge pull request #147 from genomic-medicine-sweden/drop_db 

    Adds possibility to make drop database
    @Lucpen
    Lucpen authored Oct 11, 2024
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Commits on Oct 13, 2024

  1. Template update for nf-core/tools version 3.0.2

    Lucpen committed Oct 13, 2024
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  2. fix conflicts

    Lucpen committed Oct 13, 2024
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  3. fix linting

    Lucpen committed Oct 13, 2024
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  4. fix linting

    Lucpen committed Oct 13, 2024
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  5. fix linting

    Lucpen committed Oct 13, 2024
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  6. fix subworkflows called twice

    Lucpen committed Oct 13, 2024
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  7. fix schema draft http://json-schema.org/draft-07/schema

    Lucpen committed Oct 13, 2024
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  8. updated CHANGELOG

    Lucpen committed Oct 13, 2024
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  9. fix Validation of file failed

    Lucpen committed Oct 13, 2024
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  10. fix nextflow.script.ScriptBinding.check_max()

    Lucpen committed Oct 13, 2024
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  11. Retrigger test

    Lucpen committed Oct 13, 2024
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  12. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  13. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  14. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  15. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  16. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  17. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  18. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  19. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  20. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  21. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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  22. try to fix ci.yml

    Lucpen committed Oct 13, 2024
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Commits on Oct 14, 2024

  1. try to fix ci.yml

    Lucpen committed Oct 14, 2024
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  2. try to fix ci.yml

    Lucpen committed Oct 14, 2024
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  3. try to fix ci.yml

    Lucpen committed Oct 14, 2024
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  4. Apply suggestions from code review 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Oct 14, 2024
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  5. Update nextflow.config

    @Lucpen
    Lucpen authored Oct 14, 2024
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  6. fix spacing

    Lucpen committed Oct 14, 2024
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  7. added comment on multiqc

    Lucpen committed Oct 14, 2024
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  8. fix config

    Lucpen committed Oct 14, 2024
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  9. Merge pull request #167 from genomic-medicine-sweden/TEMPLATE 

    Template update for nf-core/tools version 3.0.2
    @Lucpen
    Lucpen authored Oct 14, 2024
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Commits on Oct 15, 2024

  1. Merge

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  2. Cleaning up additional changes

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  3. Remove config link

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  4. Changelog and remove link to cmd config

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  5. Making the sex col optional

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  6. Changelog again

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  7. Clean up for testing

    @Jakob37
    Jakob37 committed Oct 15, 2024
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  8. add skip_variant_calling

    Lucpen committed Oct 15, 2024
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  9. Update conf/test.config

    @Lucpen
    Lucpen authored Oct 15, 2024
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  10. Update metromap

    Lucpen committed Oct 15, 2024
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  11. update ci.yml

    Lucpen committed Oct 15, 2024
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  12. update .nf-core.yml

    Lucpen committed Oct 15, 2024
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  13. Update CHANGELOG.md

    @Lucpen
    Lucpen authored Oct 15, 2024
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  14. apply reviewers comments

    Lucpen committed Oct 15, 2024
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  15. merge with github version

    Lucpen committed Oct 15, 2024
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  16. Merge pull request #169 from genomic-medicine-sweden/switch_variant_call 

    add parameter --skip_variant_calling
    @Lucpen
    Lucpen authored Oct 15, 2024
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  17. make module_to_export_counts_folder

    Lucpen committed Oct 15, 2024
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  18. fix training whitespace

    Lucpen committed Oct 15, 2024
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  19. fix script

    Lucpen committed Oct 15, 2024
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  20. fix training whitespace

    Lucpen committed Oct 15, 2024
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  21. fix script

    Lucpen committed Oct 15, 2024
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  22. prettify script

    Lucpen committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. add changelog

    Lucpen committed Oct 16, 2024
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  2. Apply suggestions from code review

    @Lucpen
    Lucpen authored Oct 16, 2024
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  3. turn bash script into python

    Lucpen committed Oct 16, 2024
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  4. fix script

    Lucpen committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. Merge and update changelog

    @Jakob37
    Jakob37 committed Oct 17, 2024
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  2. NA as default and non-required sex col

    @Jakob37
    Jakob37 committed Oct 17, 2024
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  3. Apply suggestions from code review 

    Co-authored-by: Peter Pruisscher <[email protected]>
    @Lucpen @peterpru
    Lucpen and peterpru authored Oct 17, 2024
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  4. Apply suggestions from code review 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Oct 17, 2024
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  5. Merge pull request #172 from genomic-medicine-sweden/module_to_export… 

    …_counts_folder

make module_to_export_counts_folder
    @Lucpen
    Lucpen authored Oct 17, 2024
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  6. initial fixes

    Lucpen committed Oct 17, 2024
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  7. initial fixes

    Lucpen committed Oct 17, 2024
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  8. Merge

    @Jakob37
    Jakob37 committed Oct 17, 2024
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  9. fix versions in verions.yml and multiqc

    Lucpen committed Oct 17, 2024
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  10. fix versions in verions.yml and multiqc

    Lucpen committed Oct 17, 2024
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  11. Add authors to pipeline

    Lucpen committed Oct 17, 2024
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  12. fix version

    Lucpen committed Oct 17, 2024
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  13. run prettier

    Lucpen committed Oct 17, 2024
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  14. Apply suggestions from code review 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Oct 17, 2024
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  15. Merge pull request #174 from genomic-medicine-sweden/fix_versions_drop 

    Fix versions in multiqc and ymls for drop modules
    @Lucpen
    Lucpen authored Oct 17, 2024
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  16. Schema help text update

    @Jakob37
    Jakob37 committed Oct 17, 2024
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  17. Merge remote-tracking branch 'github/dev' into jw-sex_info_to_drop

    @Jakob37
    Jakob37 committed Oct 17, 2024
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  18. Update changelog

    @Jakob37
    Jakob37 committed Oct 17, 2024
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  19. Merge pull request #168 from Clinical-Genomics-Lund/jw-sex_info_to_drop 

    Sex info to DROP
    @Lucpen
    Lucpen authored Oct 17, 2024
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Commits on Oct 29, 2024

  1. Updated modules

    Lucpen committed Oct 29, 2024
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  2. modified CHANGELOG

    Lucpen committed Oct 29, 2024
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  3. modified CHANGELOG

    Lucpen committed Oct 29, 2024
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  4. Update CHANGELOG.md

    @Lucpen
    Lucpen authored Oct 29, 2024
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  5. Update subworkflows/local/call_variants.nf 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Oct 29, 2024
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  6. change name of variable

    Lucpen committed Oct 29, 2024
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  7. Merge pull request #177 from genomic-medicine-sweden/prepare_release 

    Prepare release 3.0.0
    @Lucpen
    Lucpen authored Oct 29, 2024
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Commits on Nov 7, 2024

  1. add documentation

    Lucpen committed Nov 7, 2024
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  2. update CHANGELOG

    Lucpen committed Nov 7, 2024
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  3. run prettier

    Lucpen committed Nov 7, 2024
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  4. Apply suggestions from code review 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Nov 7, 2024
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  5. Merge pull request #178 from genomic-medicine-sweden/documentation 

    Add documentation
    @Lucpen
    Lucpen authored Nov 7, 2024
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  6. bump version

    Lucpen committed Nov 7, 2024
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  7. Merge pull request #180 from genomic-medicine-sweden/prepare_release 

    bump to version 3.0.0
    @Lucpen
    Lucpen authored Nov 7, 2024
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Commits on Nov 12, 2024

  1. fix bcf norm

    Lucpen committed Nov 12, 2024
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  2. line end

    Lucpen committed Nov 12, 2024
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  3. fix bug

    Lucpen committed Nov 12, 2024
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  4. Update CHANGELOG.md

    @Lucpen
    Lucpen authored Nov 12, 2024
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  5. prettier

    Lucpen committed Nov 12, 2024
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  6. Merge pull request #182 from genomic-medicine-sweden/fix_bcf_norm 

    fix bug running variant calling gatk and fix dev bug in bcf norm
    @Lucpen
    Lucpen authored Nov 12, 2024
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Commits on Nov 13, 2024

  1. change_way_adding_variant_caller to vcf

    Lucpen committed Nov 13, 2024
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  2. Update CHANGELOG.md

    @Lucpen
    Lucpen authored Nov 13, 2024
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  3. remove foundin.hdr

    Lucpen committed Nov 13, 2024
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  4. fix

    Lucpen committed Nov 13, 2024
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  5. fix

    Lucpen committed Nov 13, 2024
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  6. Update CHANGELOG.md

    @Lucpen
    Lucpen authored Nov 13, 2024
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  7. Update CHANGELOG.md 

    Co-authored-by: Felix Lenner <[email protected]>
    @Lucpen @fellen31
    Lucpen and fellen31 authored Nov 13, 2024
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  8. remove bcftools/annotate

    Lucpen committed Nov 13, 2024
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  9. change

    Lucpen committed Nov 13, 2024
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  10. prettier

    Lucpen committed Nov 13, 2024
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Commits on Nov 14, 2024

  1. Merge pull request #184 from genomic-medicine-sweden/change_way_addin… 

    …g_variant_caller

change way of adding variant caller to vcf
    @Lucpen
    Lucpen authored Nov 14, 2024
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Commits on Nov 18, 2024

  1. Update CHANGELOG.md

    @Lucpen
    Lucpen authored Nov 18, 2024
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