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Published 20 hours ago • verified publisher icon broadinstitute

Adding pipeline for Long Reads Array Data

Open jonn-smith opened this issue 3 years ago • 1 comments

  • Adding in tasks for pulling out sub-regions and updating main wdl.

  • Adding in wdl for Transcript Isoform Analysis.

  • Updated 10x Array pipeline for wider sharding.

  • Added FLAIR WDL Tasks.

  • Updated array splitting WDL.

  • Fixed issue with AlignReads.Minimap2 where if multiple bam files were given, samtools would error out.

  • Adding in metrics collection for PB10xMasSeqArraySingleFlowcell

  • Added in a task to fix CCS bams for call caching.

  • Added CleanCCSBamHeader task to clean the program group from temporary path information that is added by cromwell.

  • Added 10x tool to the PB10xCCSArraySingleFlowcell workflow.

  • Fixed a bug in the alignment task for bam files.

  • Restructured call caching code fix for CCS process.

  • Added in static MASSeq QC notebook.

  • Added PDF output MASSeq QC notebook (in addition to the HTML)

jonn-smith avatar Nov 05 '20 21:11 jonn-smith

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