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Removed pairwise batch effect checks from WDL workflow #617

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Removed pairwise batch effect checks from WDL workflow #617

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Commits on Jan 6, 2023

  1. add toggle for unstable af filter during label step in batch effect

    @epiercehoffman
    epiercehoffman committed Jan 6, 2023
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Commits on Jan 23, 2023

  1. skip AF comparison and filtering if no input provided

    @epiercehoffman
    epiercehoffman committed Jan 23, 2023
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  2. make af input actually optional

    @epiercehoffman
    epiercehoffman committed Jan 23, 2023
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Commits on Nov 9, 2023

  1. Removed pairwise batch effect checks from WDL workflow

    @shadizaheri
    shadizaheri committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. no_pairwise_no_unstable_af_filter

    @shadizaheri
    shadizaheri committed Nov 10, 2023
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Commits on Nov 17, 2023

  1. Merge branch 'eph_turn_off_unstable_af_filter' into sz_no_pairwise_ba… 

    …tch_effect
    @shadizaheri
    shadizaheri committed Nov 17, 2023
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Commits on Nov 20, 2023

  1. updated the related wdl and R script

    @shadizaheri
    shadizaheri committed Nov 20, 2023
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  2. updated the related wdl and deleted the copy of the wdl

    @shadizaheri
    shadizaheri committed Nov 20, 2023
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Commits on Nov 29, 2023

  1. Update make_batch_effect_reclassification_table.PCRMinus_only.R 

    # Just use onevsall.fails directly.
merged <- onevsall.fails
    @shadizaheri
    shadizaheri committed Nov 29, 2023
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  2. Update Module07XfBatchEffect.wdl 

    adjust tab spaces
    @shadizaheri
    shadizaheri committed Nov 29, 2023
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  3. Update Module07XfBatchEffect.wdl

    @shadizaheri
    shadizaheri committed Nov 29, 2023
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Commits on Dec 1, 2023

  1. Update make_batch_effect_reclassification_table.PCRMinus_only.R 

    analyze.failures ----> categorize.failures
    @shadizaheri
    shadizaheri committed Dec 1, 2023
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