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Pull requests: broadinstitute/long-read-pipelines

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Pull requests list

Added stand-alone RemoveSingleOrganismContamination workflow to dockstore
#500 opened May 26, 2025 by jonn-smith Loading…
Improvement: Add WDL Workflow for Automated IGV Screenshots with Customizable Resources and Inputs
#472 opened Sep 18, 2024 by shadizaheri • Draft
Add WDL script for normalizing VCF files by removing HAPCOMP and HAPDOM fields"
#470 opened Sep 15, 2024 by shadizaheri • Draft
Add initial IGV_HaplotypeViz WDL workflow for generating IGV screenshots
#468 opened Sep 5, 2024 by shadizaheri • Draft
to split vcf
#465 opened Aug 11, 2024 by shadizaheri • Draft
Adding a WDL to run DORADO for basecalling ONT data
#462 opened Jul 31, 2024 by jamesemery Loading…
Add Coverage Statistics Calculation Script for Mosdepth
#460 opened Jul 26, 2024 by bshifaw Loading…
5
Increase Maximum Cycle Value for Base Recalibrator
#459 opened Jul 26, 2024 by shadizaheri • Draft
Add BarcodeExtractor workflow to extract the barcodes from each inut_bam
#458 opened Jul 24, 2024 by shadizaheri • Draft
Sz dyst peaker
#457 opened Jul 24, 2024 by shadizaheri Loading…
mosdepth cov stat
#454 opened May 20, 2024 by bshifaw Loading…
3
Sz liftover based pmicp main
#452 opened May 5, 2024 by shadizaheri • Draft
Merging development branch from Malaria project - decontamination, pipelines for organisms with no variant truth set, etc.
#451 opened Apr 24, 2024 by brosula Loading…
Sz add mem disk aligned metrics
#448 opened Apr 23, 2024 by shadizaheri Loading…
2
Auto-Save Index Files Alongside BAMs
#446 opened Apr 11, 2024 by shadizaheri Loading…
Refine Contamination Analysis Workflow for Extra Input Resources
#443 opened Feb 29, 2024 by shadizaheri Loading…
Follow up to PR #418
#430 opened Oct 13, 2023 by SHuang-Broad Loading…
@SHuang-Broad
9
a little cleanup
#422 opened Sep 6, 2023 by tedsharpe Loading…
@tedsharpe
16
a docker image to be used for creating Terra cloud environment
#421 opened Aug 30, 2023 by SHuang-Broad Loading…
@SHuang-Broad
5
Automated WDL Testing
#420 opened Aug 24, 2023 by bshifaw Loading…
@bshifaw
1
Pipeline for ingesting high-coverage PB/ONT aligned BAMs and format them for re-processing
#418 opened Aug 18, 2023 by SHuang-Broad Loading…
@SHuang-Broad
62
Hangsu phasing
#417 opened Aug 16, 2023 by hangsuUNC • Draft
Add TRGT Special-purpose caller
#412 opened Jul 20, 2023 by mdanzi Loading…
@mdanzi
10
Adding Script to Generate a Summary of Docker Images Used by Workflows
#410 opened May 19, 2023 by bshifaw Loading…
@bshifaw
16
update Dockerfile and Makefile for Canu version update. add parameter in Canu.wdl.
#376 opened Nov 23, 2022 by eviewan • Draft
@kvg
7
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