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ChIP-seq update to 2.1.6 #528

Merged
merged 24 commits into from
Sep 5, 2023
Merged

ChIP-seq update to 2.1.6 #528

merged 24 commits into from
Sep 5, 2023

Commits on Jun 16, 2022

  1. set input files for aln wf as [[File]] rather than [[[File]]] to matc… 

    …h new wdl
    @clarabakker
    clarabakker committed Jun 16, 2022
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Commits on Jun 22, 2022

  1. set checks to use new workflows, testing

    @clarabakker
    clarabakker committed Jun 22, 2022
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  2. restore workflow specs (changed wf instead to match existing wf names… 

    …), updated wf version list
    @clarabakker
    clarabakker committed Jun 22, 2022
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  3. added wf v1.1.2-specific parameters, specified new wf uuid in wfrset_… 

    …utils
    @clarabakker
    clarabakker committed Jun 22, 2022
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  4. bracket mismatch typo

    @clarabakker
    clarabakker committed Jun 22, 2022
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  5. chip parameter step1/1c typo

    @clarabakker
    clarabakker committed Jun 22, 2022
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Commits on Jun 24, 2022

  1. further simplify fastqs input array, set reference files with names w… 

    …hich work in other ff envs
    @clarabakker
    clarabakker committed Jun 24, 2022
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Commits on Jun 30, 2022

  1. ChIP check I/O and parameters modifications for aln (ctl) and post-al… 

    …n wfs
    @clarabakker
    clarabakker committed Jun 30, 2022
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  2. add back original to accepted versions

    @clarabakker
    clarabakker committed Jun 30, 2022
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Commits on Jul 7, 2022

  1. change chip-seq to use wdl's control parameters (rm ctl prefix from f… 

    …astqs)
    @clarabakker
    clarabakker committed Jul 7, 2022
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Commits on Jul 8, 2022

  1. override benchmarking for chip ctl wf

    @clarabakker
    clarabakker committed Jul 8, 2022
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Commits on Jul 21, 2022

  1. added bool to get_chip_files to allow different endedness; updated us… 

    …age in wfr_encode checks
    @clarabakker
    clarabakker committed Jul 21, 2022
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Commits on Jul 29, 2022

  1. change paired array to booleans for ChIP-seq post-align

    @clarabakker
    clarabakker committed Jul 29, 2022
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Commits on Aug 8, 2022

  1. update ChIP-seq pipeline versions

    @clarabakker
    clarabakker committed Aug 8, 2022
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Commits on Aug 18, 2022

  1. Merge branch 'master' into chip-update

    @clarabakker
    clarabakker committed Aug 18, 2022
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Commits on Dec 2, 2022

  1. adjustments for ChIP-seq benchmarking, new WDL parameters for paired … 

    …endedness
    @clarabakker
    clarabakker committed Dec 2, 2022
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Commits on Dec 5, 2022

  1. Merge branch 'master' into chip-update

    @clarabakker
    clarabakker committed Dec 5, 2022
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Commits on Mar 27, 2023

  1. qc get failure handling

    @clarabakker
    clarabakker committed Mar 27, 2023
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  2. Merge branch 'master' into chip-update

    @clarabakker
    clarabakker committed Mar 27, 2023
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  3. Merge branch 'master' into chip-update

    @clarabakker
    clarabakker committed Mar 27, 2023
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Commits on Aug 17, 2023

  1. Merge branch 'master' into chip-update

    Ubuntu committed Aug 17, 2023
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Commits on Aug 29, 2023

  1. identify mixed paired/single ended, general cleanup

    Ubuntu committed Aug 29, 2023
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  2. Merge branch 'master' into chip-update

    @clarabakker
    clarabakker committed Aug 29, 2023
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  3. version, changelog, minor spacing fix

    @clarabakker
    clarabakker committed Aug 29, 2023
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