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Merge discvr-24.7 to develop #310

Merged
merged 42 commits into from
Aug 28, 2024
Merged

Merge discvr-24.7 to develop #310

merged 42 commits into from
Aug 28, 2024

Commits on Aug 2, 2024

  1. Show cellranger version 

    - also rename multi-chain TRA-DV segments
    @bbimber
    bbimber committed Aug 2, 2024
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Commits on Aug 4, 2024

  1. Improve handling of TRA-DV lineages

    @bbimber
    bbimber committed Aug 4, 2024
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  2. Move getLocationForCachedInputs to SequenceJob

    @bbimber
    bbimber committed Aug 4, 2024
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  3. Allow alignment jobs to re-download archived SRA data

    @bbimber
    bbimber committed Aug 4, 2024
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  4. Bugfix to handling of TRAV/DV segments

    @bbimber
    bbimber committed Aug 4, 2024
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  5. Bugfix when doSraDownloadIfNeeded not provided

    @bbimber
    bbimber committed Aug 4, 2024
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  6. Primers should not be required for CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 4, 2024
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  7. Primers are required for CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 4, 2024
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  8. Allow client-side to accept SRA archived data

    @bbimber
    bbimber committed Aug 4, 2024
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Commits on Aug 5, 2024

  1. Set job status in SequenceAlignmentTask

    @bbimber
    bbimber committed Aug 5, 2024
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  2. Improve cellranger description fields

    @bbimber
    bbimber committed Aug 5, 2024
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  3. Bugfix to cached ReadData

    @bbimber
    bbimber committed Aug 5, 2024
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Commits on Aug 7, 2024

  1. Ensure SRA data not deleted until end of job

    @bbimber
    bbimber committed Aug 7, 2024
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  2. Update AppendCiteSeq for newer versions

    @bbimber
    bbimber committed Aug 7, 2024
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  3. Support minAllowableDoubletRateFilter

    @bbimber
    bbimber committed Aug 7, 2024
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  4. Do more cleanup in CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. Bugfix SRA download

    @bbimber
    bbimber committed Aug 8, 2024
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  2. Bugfix to cell hashing command

    @bbimber
    bbimber committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Push RIRA logic into R package

    @bbimber
    bbimber committed Aug 9, 2024
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Commits on Aug 10, 2024

  1. Bugfix to MergeBamAlignment

    @bbimber
    bbimber committed Aug 10, 2024
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Commits on Aug 13, 2024

  1. More verbose logging in CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. Skip duplicated SRA accessions when re-downloading

    @bbimber
    bbimber committed Aug 14, 2024
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Commits on Aug 16, 2024

  1. Update defaults for CellRangerGexCountStep

    @bbimber
    bbimber committed Aug 16, 2024
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  2. Allow seurat pipeline to be kicked off against 10x Run Summaries

    @bbimber
    bbimber committed Aug 16, 2024
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Commits on Aug 20, 2024

  1. Bugfix to UpdateReadsetFilesHandler

    @bbimber
    bbimber committed Aug 20, 2024
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  2. Bugfix to AppendCiteSeq

    @bbimber
    bbimber committed Aug 20, 2024
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  3. Bugfix to UpdateReadsetFilesHandler

    @bbimber
    bbimber committed Aug 20, 2024
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Commits on Aug 24, 2024

  1. Bugfix to CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 24, 2024
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Commits on Aug 25, 2024

  1. Bugfix to CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 25, 2024
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  2. Allow CellRanger to more easily skip BAM creation

    @bbimber
    bbimber committed Aug 25, 2024
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  3. Allow CellRangerVDH to more easily skip BAM creation

    @bbimber
    bbimber committed Aug 25, 2024
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  4. Second fix for alignments that dont produce BAMs

    @bbimber
    bbimber committed Aug 25, 2024
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Commits on Aug 26, 2024

  1. Fix for alignments that dont produce BAMs

    @bbimber
    bbimber committed Aug 26, 2024
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  2. Ensure cellranger-dependent steps retain BAM

    @bbimber
    bbimber committed Aug 26, 2024
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  3. Bugfix to BAM-less jobs

    @bbimber
    bbimber committed Aug 26, 2024
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  4. Update CellRanger metrics for BAM-less jobs

    @bbimber
    bbimber committed Aug 26, 2024
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  5. Bugfix to FeaturePlots.R when tsne not present

    @bbimber
    bbimber committed Aug 26, 2024
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  6. Add validation to Cell Ranger steps

    @bbimber
    bbimber committed Aug 26, 2024
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  7. Change order of steps when no BAM present

    @bbimber
    bbimber committed Aug 26, 2024
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  8. Reduce log level when BAM is discarded

    @bbimber
    bbimber committed Aug 26, 2024
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Commits on Aug 28, 2024

  1. Walk back create-bam arg in CellRangerVDJWrapper

    @bbimber
    bbimber committed Aug 28, 2024
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  2. Merge discvr-24.7 to develop

    @bbimber
    bbimber committed Aug 28, 2024
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