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Follow up to PR #418#430

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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 19, 2023

• New workflows

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Commits on Dec 27, 2023

• Improve various existing codes

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• New workflow to save files (avoid multiple calls to Finalize)

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• New workflow to unify QC and metrics collection on aligned BAM

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• Update grouping of pipelines in .dockstore.yml

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• update WDL validation bash script

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Commits on Dec 28, 2023

• DEPRECATION

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Commits on Jan 2, 2024

• Fix bug in deduplicating aligned ONT BAM

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Commits on Jan 3, 2024

• DEPRECATION:

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• Update utility code:

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Commits on Jan 12, 2024

• a few tweaks to to AlignedBamQCandMetrics:

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Commits on Jan 18, 2024

• correct two mistakes: 1. a typo; 2. should append not replace

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Commits on Jan 22, 2024

• make read-length util tasks pre-emptible

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Commits on Jan 23, 2024

• make fingerprint reads extraction more efficient/resilient

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• fix a stupid logical typo error (in saving files)

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Commits on Jan 31, 2024

• option to force run fingerprintcheck on small bams

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Commits on Feb 2, 2024

• make pbindex task more frugal

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Commits on Mar 1, 2024

• Safer and more efficient way to do targetted pileup conversion

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• Update Pacbio alignment task

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• New subworkflow to align PacBio uBAM

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• Two new workflows:

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Commits on Mar 7, 2024

• bug fix for bam2fastq

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Commits on Jun 25, 2024

• optimize alignment further

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Commits on Jul 17, 2024

• test reducing resources for pbmm2 further

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