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Add module bcftools/norm to sarek (in progress) #1483

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Add module bcftools/norm to sarek (in progress) #1483

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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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