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Picard: directly support Sentieon #2110

Merged
merged 39 commits into from
Nov 13, 2023
Merged

Picard: directly support Sentieon #2110

merged 39 commits into from
Nov 13, 2023

Commits on Oct 11, 2023

  1. Reuse picard AlignmentSummary and GcBias funcs for Sentieon

    @vladsavelyev
    vladsavelyev committed Oct 11, 2023
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Commits on Oct 12, 2023

  1. [automated] Update CHANGELOG.md

    @multiqc-bot
    multiqc-bot committed Oct 12, 2023
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  2. Refactor to reuse all Picard modules for Sentieon

    @vladsavelyev
    vladsavelyev committed Oct 12, 2023
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Commits on Oct 13, 2023

  1. Refactor more

    @vladsavelyev
    vladsavelyev committed Oct 13, 2023
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Commits on Oct 17, 2023

  1. WIP

    @vladsavelyev
    vladsavelyev committed Oct 17, 2023
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Commits on Oct 19, 2023

  1. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  2. Remover sentieon module, make sure picard module supports both

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  3. Check tool/algo name as well

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  4. Fix GcBiasMetrics

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  5. Adjust WgsMetrics, MarkDuplicates, InsertSizeMetrics, GcBiasMetrics

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  6. Fix hists

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  7. Adjust Quality* modules

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  8. Fixes

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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  9. Add add_software_version calls

    @vladsavelyev
    vladsavelyev committed Oct 19, 2023
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Commits on Oct 26, 2023

  1. Clean up

    @vladsavelyev
    vladsavelyev committed Oct 26, 2023
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Commits on Oct 27, 2023

  1. WIP: remove shared. Remove class methods. Add docs

    @vladsavelyev
    vladsavelyev committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Oct 30, 2023
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  2. WIP

    @vladsavelyev
    vladsavelyev committed Oct 30, 2023
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Commits on Nov 1, 2023

  1. Finalise Picard refactoring

    @vladsavelyev
    vladsavelyev committed Nov 1, 2023
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  2. Remove "shared"

    @vladsavelyev
    vladsavelyev committed Nov 1, 2023
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  3. Update changelog

    @vladsavelyev
    vladsavelyev committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. Fixes

    @vladsavelyev
    vladsavelyev committed Nov 2, 2023
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  2. Add MEDIAN_TARGET_COVERAGE to HsMetrics. Fix RnaSeqMetrics regex

    @vladsavelyev
    vladsavelyev committed Nov 2, 2023
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  3. Docs

    @vladsavelyev
    vladsavelyev committed Nov 2, 2023
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  4. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Nov 3, 2023
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Commits on Nov 4, 2023

  1. Fix sorting tables

    @vladsavelyev
    vladsavelyev committed Nov 4, 2023
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  2. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Nov 4, 2023
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  3. Update CSP

    @vladsavelyev
    vladsavelyev committed Nov 4, 2023
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Commits on Nov 6, 2023

  1. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Nov 6, 2023
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Commits on Nov 8, 2023

  1. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Nov 8, 2023
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  2. Document sample naming

    @vladsavelyev
    vladsavelyev committed Nov 8, 2023
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  3. More refactor

    @vladsavelyev
    vladsavelyev committed Nov 8, 2023
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  4. Merge reports of dif types in IlluminaLaneMetrics, readd LANE in Extr… 

    …actIlluminaBarcodes
    @vladsavelyev
    vladsavelyev committed Nov 8, 2023
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Commits on Nov 13, 2023

  1. Add CHANGELOG highlights

    @vladsavelyev
    vladsavelyev committed Nov 13, 2023
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  2. Remove more sentieon references

    @vladsavelyev
    vladsavelyev committed Nov 13, 2023
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  3. More highlights

    @vladsavelyev
    vladsavelyev committed Nov 13, 2023
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  4. More highlights

    @vladsavelyev
    vladsavelyev committed Nov 13, 2023
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  5. Merge branch 'master' into sentieon-picard

    @vladsavelyev
    vladsavelyev committed Nov 13, 2023
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