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Add cnvkit germline mode #576

Merged
merged 20 commits into from
Jun 7, 2022
Merged

Add cnvkit germline mode #576

merged 20 commits into from
Jun 7, 2022

Commits on Jun 1, 2022

  1. add cnvkit_germline

    @SusiJo
    SusiJo committed Jun 1, 2022
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  2. updated changelog [skip actions]

    @SusiJo
    SusiJo committed Jun 1, 2022
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  3. Merge remote-tracking branch 'origin/dev' into cnvkit_germline

    @SusiJo
    SusiJo committed Jun 1, 2022
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Commits on Jun 3, 2022

  1. installed new cnvkit/module

    @SusiJo
    SusiJo committed Jun 3, 2022
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  2. added new subway_map cnvkit_germline

    @SusiJo
    SusiJo committed Jun 3, 2022
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  3. add germline subworkflow + add fasta_fai

    @SusiJo
    SusiJo committed Jun 3, 2022
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  4. add fasta fai

    @SusiJo
    SusiJo committed Jun 3, 2022
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  5. add ci tests for cnvkit

    @SusiJo
    SusiJo committed Jun 3, 2022
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  6. ran prettier

    @SusiJo
    SusiJo committed Jun 3, 2022
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  7. Merge remote-tracking branch 'origin/dev' into cnvkit_germline

    @SusiJo
    SusiJo committed Jun 3, 2022
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  8. adjusted PR # in changelog

    @SusiJo
    SusiJo committed Jun 3, 2022
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  9. Update subworkflows/local/germline_variant_calling.nf 

    Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
    @SusiJo @maxulysse
    SusiJo and maxulysse authored Jun 3, 2022
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  10. rm concat + bgzip_vcf

    @SusiJo
    SusiJo committed Jun 3, 2022
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  11. add command log to output

    @FriederikeHanssen
    FriederikeHanssen committed Jun 3, 2022
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  12. log out and log err throw errors, so removed

    @FriederikeHanssen
    FriederikeHanssen committed Jun 3, 2022
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Commits on Jun 7, 2022

  1. force reinstalled cnvkit/batch from modules

    @SusiJo
    SusiJo committed Jun 7, 2022
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  2. Merge remote-tracking branch 'origin/cnvkit_germline' into cnvkit_ger… 

    …mline
    @SusiJo
    SusiJo committed Jun 7, 2022
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  3. rm - before command

    @SusiJo
    SusiJo committed Jun 7, 2022
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  4. rm - before tags and files

    @SusiJo
    SusiJo committed Jun 7, 2022
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  5. rm -

    @SusiJo
    SusiJo committed Jun 7, 2022
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