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Sarek bcftools normalization #1682

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Sarek bcftools normalization #1682

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Commits on Apr 25, 2024

  1. First modification to contribute to the bcftools/norm module in Sarek

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  2. Changes in the GERMLINE_VCFS_NORM process

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  3. Add fasta argument to POST_VARIANTCALLING process.

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  4. add fasta input as argument

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  5. remove vcfs in the GERMLINE_VCFS_NORM process, replaced by germline_v… 

    …cfs_with_tbis and fasta.
    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  6. First modification to contribute to the bcftools/norm module in Sarek

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  7. Changes in the GERMLINE_VCFS_NORM process

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  8. Add fasta argument to POST_VARIANTCALLING process.

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  9. add fasta input as argument

    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  10. remove vcfs in the GERMLINE_VCFS_NORM process, replaced by germline_v… 

    …cfs_with_tbis and fasta.
    @JC-Delmas
    JC-Delmas committed Apr 25, 2024
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  11. Update workflows/sarek/main.nf 

    resolve issue with spacing

Co-authored-by: Maxime U Garcia <[email protected]>
    @JC-Delmas @maxulysse
    JC-Delmas and maxulysse authored Apr 25, 2024
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Commits on Apr 30, 2024

  1. Resolved merge conflict by keeping changes from branch 34bf47b

    @JC-Delmas
    JC-Delmas committed Apr 30, 2024
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  2. Refactor normalization and concatenation of VCF files

    @JC-Delmas
    JC-Delmas committed Apr 30, 2024
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Commits on May 16, 2024

  1. Modify and adjust two scripts to add normalization and integrate FAST… 

    …A support
    @JC-Delmas
    JC-Delmas committed May 16, 2024
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Commits on Oct 9, 2024

  1. Added normalization for all vcfs

    @Patricie34
    Patricie34 committed Oct 9, 2024
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Commits on Oct 11, 2024

  1. Fixed linting issues and updated schema parameters

    @Patricie34
    Patricie34 committed Oct 11, 2024
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  2. Update conf/modules/post_variant_calling.config 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @Patricie34 @maxulysse
    Patricie34 and maxulysse authored Oct 11, 2024
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  3. edit of normalization steps

    @Patricie34
    Patricie34 committed Oct 11, 2024
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Commits on Oct 15, 2024

  1. Fixed linting issues

    @Patricie34
    Patricie34 committed Oct 15, 2024
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  2. Merge remote-tracking branch 'upstream/dev' into sarek_bcftools_norm

    @Patricie34
    Patricie34 committed Oct 15, 2024
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  3. Sync with dev_branch

    @Patricie34
    Patricie34 committed Oct 15, 2024
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  4. Updated CHANGELOG.md

    @Patricie34
    Patricie34 committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. Update conf/modules/post_variant_calling.config 

    Co-authored-by: Friederike Hanssen <[email protected]>
    @Patricie34 @FriederikeHanssen
    Patricie34 and FriederikeHanssen authored Oct 16, 2024
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  2. Update nextflow.config 

    Co-authored-by: Friederike Hanssen <[email protected]>
    @Patricie34 @FriederikeHanssen
    Patricie34 and FriederikeHanssen authored Oct 16, 2024
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  3. Changed module.config

    @Patricie34
    Patricie34 committed Oct 16, 2024
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  4. Changelog.md updated

    @Patricie34
    Patricie34 committed Oct 16, 2024
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  5. Fixed params.normalize

    @Patricie34
    Patricie34 committed Oct 16, 2024
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Commits on Oct 18, 2024

  1. Update CHANGELOG.md 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @Patricie34 @maxulysse
    Patricie34 and maxulysse authored Oct 18, 2024
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  2. pytesttags.yml changed

    @Patricie34
    Patricie34 committed Oct 18, 2024
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  3. edited test_normalize_vcfs.yml

    @Patricie34
    Patricie34 committed Oct 18, 2024
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Commits on Oct 22, 2024

  1. Separated vcf_normalization

    @Patricie34
    Patricie34 committed Oct 22, 2024
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Commits on Nov 4, 2024

  1. Merge branch 'dev' into sarek_bcftools_norm

    @maxulysse
    maxulysse authored Nov 4, 2024
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Commits on Nov 5, 2024

  1. module.config edited

    @Patricie34
    Patricie34 committed Nov 5, 2024
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  2. extra file removed

    @Patricie34
    Patricie34 committed Nov 5, 2024
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  3. post_variantcalling edited

    @Patricie34
    Patricie34 committed Nov 5, 2024
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  4. added annotation for vcfs_normalized

    @Patricie34
    Patricie34 committed Nov 5, 2024
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