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Dev > Master for v2.0.0 #41

Merged
merged 234 commits into from
Jul 5, 2023
Merged

Dev > Master for v2.0.0 #41

merged 234 commits into from
Jul 5, 2023

Commits on Dec 19, 2022

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Commits on Feb 2, 2023

  1. bump to 1.0dev

    mirpedrol committed Feb 2, 2023
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  2. add Zenodo DOI

    mirpedrol committed Feb 2, 2023
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  3. add Zenodo badge

    mirpedrol committed Feb 2, 2023
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  4. run prettier

    mirpedrol committed Feb 2, 2023
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Commits on Feb 3, 2023

  1. Merge pull request #14 from nf-core/master

    Add Zenodo DOI master -> dev
    mirpedrol authored Feb 3, 2023
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Commits on Feb 23, 2023

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Commits on Feb 28, 2023

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Commits on Mar 15, 2023

  1. add extract umi step

    mirpedrol committed Mar 15, 2023
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  2. add test_umis.config

    mirpedrol committed Mar 15, 2023
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Commits on Mar 16, 2023

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Commits on Mar 17, 2023

  1. fix extract_umis

    mirpedrol committed Mar 17, 2023
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  2. install vsearch

    mirpedrol committed Mar 17, 2023
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Commits on Mar 20, 2023

  1. add vsearch/cluster step

    mirpedrol committed Mar 20, 2023
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Commits on Mar 21, 2023

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Commits on Mar 24, 2023

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Commits on Apr 5, 2023

  1. install vsearch/sort

    mirpedrol committed Apr 5, 2023
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  2. add umi_bin_size parameter

    mirpedrol committed Apr 5, 2023
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Commits on Apr 6, 2023

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  3. install new module racon

    mirpedrol committed Apr 6, 2023
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  4. add racon

    mirpedrol committed Apr 6, 2023
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Commits on Apr 25, 2023

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Commits on Apr 28, 2023

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Commits on May 3, 2023

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  3. Merge pull request #13 from mirpedrol/bump-1.0dev

    Bump to 1.1dev
    mirpedrol authored May 3, 2023
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Commits on May 4, 2023

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  5. remove mandatory input

    LaurenceKuhl committed May 4, 2023
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Commits on May 5, 2023

  1. fix bug returning only one sequence from UMI cluster and filter UMI a…

    …lignments to ignore empty alignments
    mirpedrol committed May 5, 2023
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  3. update changelog

    mirpedrol committed May 5, 2023
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  5. update changelog

    mirpedrol committed May 5, 2023
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  6. add test_umi tests to CI

    mirpedrol committed May 5, 2023
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  7. install medaka

    mirpedrol committed May 5, 2023
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  8. install samtools/faidx

    mirpedrol committed May 5, 2023
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Commits on May 8, 2023

  1. run faidx

    mirpedrol committed May 8, 2023
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Commits on May 9, 2023

  1. add minimap and samtools for mini_align process

    Julia Mir Pedrol committed May 9, 2023
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  2. remove mini_align as it's now performed by medaka_consensus

    Julia Mir Pedrol committed May 9, 2023
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  3. add medaka process

    Julia Mir Pedrol committed May 9, 2023
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Commits on May 11, 2023

  1. unzip input medaka

    mirpedrol committed May 11, 2023
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Commits on May 15, 2023

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  3. unzip medaka input

    mirpedrol committed May 15, 2023
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  4. fix medaka error

    mirpedrol committed May 15, 2023
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Commits on May 16, 2023

  1. Update conf/modules.config

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    LaurenceKuhl and mirpedrol authored May 16, 2023
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Commits on May 17, 2023

  1. Update main.nf

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    LaurenceKuhl and mirpedrol authored May 17, 2023
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  2. Update workflows/crisprseq_screening.nf

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    LaurenceKuhl and mirpedrol authored May 17, 2023
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  3. Update workflows/crisprseq_screening.nf

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    LaurenceKuhl and mirpedrol authored May 17, 2023
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  6. Fix nextflow schema

    LaurenceKuhl committed May 17, 2023
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  10. Ran prettier

    LaurenceKuhl committed May 17, 2023
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  11. fix indentation

    LaurenceKuhl committed May 17, 2023
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Commits on May 22, 2023

  1. hopefully fix umis bug

    mirpedrol committed May 22, 2023
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Commits on May 23, 2023

  1. tiny markdown fixes

    Some tiny markdown errors I found while looking too long at this page for a certain website.
    mashehu authored May 23, 2023
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Commits on May 24, 2023

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  2. Merge pull request #26 from nf-core/smaller-md-fixes

    tiny markdown fixes
    mashehu authored May 24, 2023
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Commits on May 25, 2023

  1. run prettier

    mirpedrol committed May 25, 2023
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  2. ignore actions_ci test

    mirpedrol committed May 25, 2023
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  4. Merge pull request #22 from LaurenceKuhl/master

    Adding functional genomics
    LaurenceKuhl authored May 25, 2023
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Commits on May 26, 2023

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  3. fix analysis screening

    mirpedrol committed May 26, 2023
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Commits on May 30, 2023

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Commits on Jun 2, 2023

  1. Documentation

    LaurenceKuhl committed Jun 2, 2023
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Commits on Jun 5, 2023

  1. Documentation

    LaurenceKuhl committed Jun 5, 2023
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  2. Merge pull request #1 from nf-core/screening

    Screening
    LaurenceKuhl authored Jun 5, 2023
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  3. Documentation

    LaurenceKuhl committed Jun 5, 2023
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Commits on Jun 6, 2023

  1. Documentation

    LaurenceKuhl committed Jun 6, 2023
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  2. Ran prettier

    LaurenceKuhl committed Jun 6, 2023
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  3. Merge pull request #27 from mirpedrol/merge-workflows

    Merge workflows targeted & screening
    mirpedrol authored Jun 6, 2023
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  5. Merge pull request #29 from LaurenceKuhl/master

    Add documentation
    LaurenceKuhl authored Jun 6, 2023
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  7. Merge pull request #25 from mirpedrol/fix-module-warning

    alias all includes of MINIMAP2_ALIGN
    mirpedrol authored Jun 6, 2023
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Commits on Jun 7, 2023

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  5. fix spacing for Júlia

    LaurenceKuhl committed Jun 7, 2023
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  7. Merge pull request #31 from LaurenceKuhl/master

    change name of certain params for more clarity
    mirpedrol authored Jun 7, 2023
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  8. docs review

    mirpedrol committed Jun 7, 2023
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  11. split docs

    mirpedrol committed Jun 7, 2023
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Commits on Jun 8, 2023

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Commits on Jun 9, 2023

  1. Merge pull request #32 from mirpedrol/screening

    Review Docs from #30
    mirpedrol authored Jun 9, 2023
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  5. title correction

    LaurenceKuhl committed Jun 9, 2023
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  7. Merge pull request #33 from LaurenceKuhl/master

    crisprcleanr output added in the main.nf and docs
    LaurenceKuhl authored Jun 9, 2023
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  8. Update docs/output_screening.md

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    LaurenceKuhl and mirpedrol authored Jun 9, 2023
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  10. Merge pull request #30 from nf-core/screening

    Add screening analysis
    LaurenceKuhl authored Jun 9, 2023
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Commits on Jun 12, 2023

  1. Merge branch 'umi-clustering' of https://github.com/mirpedrol/crisprseq

    … into mirpedrol-umi-clustering
    mirpedrol committed Jun 12, 2023
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  4. fix typo

    mirpedrol committed Jun 12, 2023
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  5. update schema

    mirpedrol committed Jun 12, 2023
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  8. run prettier [ci skip]

    mirpedrol committed Jun 12, 2023
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  9. Merge pull request #34 from mashehu/new-docs-structure

    move sub-docs into subdirectories
    mirpedrol authored Jun 12, 2023
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  10. add docs for UMIs

    mirpedrol committed Jun 12, 2023
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  11. add tube map

    mirpedrol committed Jun 12, 2023
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Commits on Jun 13, 2023

  1. fix image links

    mashehu committed Jun 13, 2023
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  4. Merge pull request #36 from mashehu/new-docs-structure

    fix image links
    mirpedrol authored Jun 13, 2023
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  10. Docs

    LaurenceKuhl committed Jun 13, 2023
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  11. Merge pull request #35 from mirpedrol/add-tubemap

    add tube map
    mirpedrol authored Jun 13, 2023
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  13. Update CHANGELOG.md

    mirpedrol authored Jun 13, 2023
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Commits on Jun 14, 2023

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  4. oups

    LaurenceKuhl committed Jun 14, 2023
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  5. Merge pull request #37 from LaurenceKuhl/master

    Full screening config file for aws
    mirpedrol authored Jun 14, 2023
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  6. Merge pull request #39 from mashehu/change-tubemap-tag

    use new github style of dark mode images
    mirpedrol authored Jun 14, 2023
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Commits on Jun 15, 2023

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Commits on Jun 16, 2023

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  2. Apply suggestions from code review

    Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
    mirpedrol and SusiJo authored Jun 16, 2023
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  10. change matrix name

    mirpedrol committed Jun 16, 2023
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  11. add pre-commit

    mirpedrol committed Jun 16, 2023
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  12. run prettier

    mirpedrol committed Jun 16, 2023
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  13. add black and isort

    mirpedrol committed Jun 16, 2023
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Commits on Jun 19, 2023

  1. add crispr-A citation

    mirpedrol committed Jun 19, 2023
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  2. run prettier

    mirpedrol committed Jun 19, 2023
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Commits on Jun 22, 2023

  1. Merge pull request #42 from mirpedrol/improve-docs

    Improve docs
    mirpedrol authored Jun 22, 2023
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Commits on Jun 26, 2023

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Commits on Jun 27, 2023

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  3. update changelog

    mirpedrol committed Jun 27, 2023
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  6. Merge pull request #44 from mirpedrol/release-review

    Release review
    mirpedrol authored Jun 27, 2023
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  13. fix alias SEQTK_SEQ_MASK

    mirpedrol committed Jun 27, 2023
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Commits on Jun 28, 2023

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  4. Merge branch 'dev' of https://github.com/nf-core/crisprseq into nf-co…

    …re-template-merge-2.8
    mirpedrol committed Jun 28, 2023
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  5. update modules

    mirpedrol committed Jun 28, 2023
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  7. update changelog

    mirpedrol committed Jun 28, 2023
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  8. update changelog

    mirpedrol committed Jun 28, 2023
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  9. apply review comments

    mirpedrol committed Jun 28, 2023
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  10. Merge pull request #47 from LaurenceKuhl/master

    Add mageck and crisprcleanr in the citations
    LaurenceKuhl authored Jun 28, 2023
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  11. Merge pull request #45 from mirpedrol/reference-param

    Add new parameters `--reference` and `--protospacer`
    mirpedrol authored Jun 28, 2023
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  12. Merge pull request #48 from mirpedrol/aws-fulltest-yml

    Split AWS fulltests in two separate files
    mirpedrol authored Jun 28, 2023
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  14. Merge pull request #24 from mirpedrol/umi-clustering

    Add UMI clustering
    mirpedrol authored Jun 28, 2023
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  15. Merge branch 'dev' of https://github.com/nf-core/crisprseq into nf-co…

    …re-template-merge-2.8
    mirpedrol committed Jun 28, 2023
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  17. Merge pull request #21 from nf-core/nf-core-template-merge-2.8

    Important! Template update for nf-core/tools v2.8
    mirpedrol authored Jun 28, 2023
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  19. update date

    mirpedrol committed Jun 28, 2023
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  20. Merge pull request #38 from mirpedrol/bump-2.0.0

    bump version to 2.0.0 and update changelog
    mirpedrol authored Jun 28, 2023
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  22. remove profile aws_tower

    mirpedrol committed Jun 28, 2023
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  25. remove registry form config

    mirpedrol committed Jun 28, 2023
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  27. update changelog

    mirpedrol committed Jun 28, 2023
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  28. Apply suggestions from code review

    Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
    mirpedrol and SusiJo authored Jun 28, 2023
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  30. Merge pull request #50 from mirpedrol/fix-full-tests-tower

    remove profile aws_tower
    mirpedrol authored Jun 28, 2023
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  31. replace exit 1 by error

    mirpedrol committed Jun 28, 2023
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  33. replace exit 1 by error

    mirpedrol committed Jun 28, 2023
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  34. Merge pull request #51 from mirpedrol/release-review

    Release review
    mirpedrol authored Jun 28, 2023
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Commits on Jul 3, 2023

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  4. Merge pull request #54 from mirpedrol/test

    Run test_Targeted when using `-profile test`
    mirpedrol authored Jul 3, 2023
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  6. Align spaces

    LaurenceKuhl committed Jul 3, 2023
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  7. Merge conflicts

    LaurenceKuhl committed Jul 3, 2023
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  8. Merge pull request #55 from LaurenceKuhl/master

    Add test_screening_full.config in the config file
    LaurenceKuhl authored Jul 3, 2023
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Commits on Jul 4, 2023

  1. fix id in normalize

    LaurenceKuhl committed Jul 4, 2023
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Commits on Jul 5, 2023

  1. Modify changelog

    LaurenceKuhl committed Jul 5, 2023
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  2. Merge pull request #56 from LaurenceKuhl/master

    fix bug full_test
    LaurenceKuhl authored Jul 5, 2023
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  3. update release date

    mirpedrol committed Jul 5, 2023
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