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Sz dyst peaker#457

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shadizaheri wants to merge 13 commits intomainbroadinstitute/long-read-pipelines:mainfrom sz_dyst_peakerbroadinstitute/long-read-pipelines:sz_dyst_peakerCopy head branch name to clipboard

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Commits on Nov 8, 2023

• UPDATES TO THE Hifiasm pipeline:

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• For both CCS/ONT, update PBSV

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• For both CCS/ONT, update Sniffles-2

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• CRITICAL: updating pbindex to that from the SMRTLink 12 release

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• MAJOR REFACTOR: UNIFY CCS/ONT WGS PIPELINE

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Commits on Dec 1, 2023

• MISC UPDATES TO SEVERAL UTILS TASKS

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• New docker that's intended to replace lr-basic:

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• New docker that offers a new mode remove duplicates from a queryname-sorted ONT bam

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• New docker that updates the samtools in GATK to the latest (1.18)

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• significantly boost capabilities of BAMutils.wdl

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• update some legacy code due to new interfaces in updated BAMutils.wdl

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Commits on Dec 4, 2023

• A heuristic way to find peaks in a distribution (using dyst)

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Commits on Jul 24, 2024

• Add saveLRArrayOutput as a main output for Terra data table

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