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CNVKit 0.9.10 update #3651

Merged
merged 10 commits into from
Jul 21, 2023
Merged

CNVKit 0.9.10 update #3651

merged 10 commits into from
Jul 21, 2023

Commits on Jun 22, 2023

  1. upgrade CNVkit to 0.9.10

    @priesgo
    priesgo committed Jun 22, 2023
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  2. homogenise keywords of all CNVkit modules

    @priesgo
    priesgo committed Jun 22, 2023
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Commits on Jul 12, 2023

  1. Add samtools dependency to bam2seqz module of sequenzautils 

    Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests)
    @JulianMohr
    JulianMohr authored Jul 12, 2023
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Commits on Jul 19, 2023

  1. Update cnvkit to 0.9.10 

    Changes:
 - Update cnvkit to 0.9.10
 - Update samtools in cnvkit modules to 1.17

Based on #3545 authored by @priesgo.
    @adamrtalbot
    adamrtalbot committed Jul 19, 2023
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  2. Merge branch 'master' into cnvkit_0.9.10_updates

    @adamrtalbot
    adamrtalbot authored Jul 19, 2023
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  3. cnvkit 0.9.10 test update

    @adamrtalbot
    adamrtalbot committed Jul 19, 2023
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Commits on Jul 21, 2023

  1. update checksums of output files in tests for CNVkit batch

    @priesgo
    priesgo committed Jul 21, 2023
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  2. Merge branch 'master' into cnvkit_0.9.10_updates

    @priesgo
    priesgo authored Jul 21, 2023
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  3. Update cnvkit/export VCF test

    @adamrtalbot
    adamrtalbot committed Jul 21, 2023
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  4. Additional tags for sequenzautils

    @adamrtalbot
    adamrtalbot committed Jul 21, 2023
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