lrp_4.0.17

Made the finalize steps optional for workflows in the srmalaria workspace. (#453)

• Made gcs_root_out_dir optional in SRFlowcell
• Made gcs_out_root_dir optional in SRWholeGenome
• Made gcs_out_root_dir optional for SRJointCallGVCFsWithGenomicsDB

lrp_4.0.16

Updated short read variant calling and joint calling pipelines to run at scale (#450)

Single-sample variant calling:

• Fixied critical typo in HaplotypeCaller disk spec.
• Fixed wdl-computed divide by zero error in SRFlowcell outputs.
• Updated MergeVCFs to have an option to name an output as a GVCF.
• Removed deprecated GC logging flags from GATK commands.
• Fixed issue in FastQC if no read qualities are in the file.
• Added missing annotation groups to ReblockGVCFs.
• HaplotypeCaller WDL now returns the reblocked GVCF.

Joint Calling:

• Added option to use gnarly genotyper
• Added het inputs to joint genotyping
• Fixed java memory allocation in joint genotyping to be based on memory of the VM, not hard-coded
• Fixed name of outdir in ConvertToZarrStore to be correct for this workflow.
• Updated the zarr conversion to use parallel Dask processes and to log to stdout.
• Upped default zarr conversion memory to 32gb.

VETS:

• Added stack trace logging for errors in ExtractVariantAnnotations,
  TrainVariantAnnotationsModel, and ScoreVariantAnnotations.
• Removed HAPCOMP, HAPDOM, and HEC from default annotations for SNP and INDEL VETS filtration on joint-called VCF files. Need to do more testing / debugging to include these in joint calling.

Misc:

• Fixed the name of the workflow in ExpandedDrugResistanceMarkerAggregation to reflect the actual name.
• Miscellaneous updates for debugging

lrp_4.0.15

make submissions folder deletion better (#445)

• make submissions folder deletion better

lrp_4.0.14

Several updates for making Malaria Joint Calling easier. (#449)

• Reintroduced ReblockGVCF step.

• Updated HaplotypeCaller::ReblockGVCF to point to latest Docker image
  with fix for ReblockGVCF annotations.
• Updated HaplotypeCaller::ReblockGVCF to use 2 cores.
• Disabled DeepVariant/Pepper calling in SRWholeGenome by default.
• Removed SRJointGenotyping::ReblockGVCF - it should only be defined
  in one place.

• Removed hard filtered output file.

• Updating all GATK 4.3 tasks to GATK 4.5

• Disabled QC when running on a singe bam file input.

• Added a runtime_attr override for HaplotypeCaller subworkflow.

• Update Utils.wdl

Modified the disks from " LOCAL" to " SSD"

• Updating tasks to use SSD rather than LOCAL disk.

• Moved HaplotypeCaller and ReblockGVCF to SSD from HDD

• Fixed a bug in compute_sr_stats.py that allowed nans

• Updated sr-utils docker to use mamba conda env solver.

• Updates to sr-utils docker image.

• Updated conda solver in sr-utils to mamba.
• Fixed minor deprecation warning in compute_sr_stats.py
• Fixed issue in compute_sr_stats.py that caused certain inputs to
  fail due to missing base qualities or nan values.
• Updated version of sr-utils docker image to 0.2.2.

• Updated sr-utils docker image to version 0.2.2

• Added note for updating nightly GATK build.

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Co-authored-by: Shadi Zaheri 74751641+shadizaheri@users.noreply.github.com

lrp_4.0.13

update dockstore cli in git action yml (#447)

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_4.0.12

Add WDL Workflow: Plots metrics for SV Calls for Multiple Samples (#438)

• SvQcplots.wdl draft

• Added concat sv stats

• added compile sv stats by sample

• added runtime in compileSVstats

• added addcoverage task

• added plotting task

• adding docker for plotting

Co-authored-by: Steve Huang shuang@broadinstitute.org

• Update wdl/pipelines/TechAgnostic/Visualization/SvQCPlots.wdl

specified bcfQuerySV task docker

Co-authored-by: Steve Huang shuang@broadinstitute.org

• add meta section to SvQCPlots.wdl

• add option to name output plot notebook SvQCPlots.wdl

• Minor additions (#444)

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Co-authored-by: Steve Huang shuang@broadinstitute.org

• update docker to ubuntu for addCoverageToSVstats

• containerized compilesvstats

• added a full path to compilesvstats.py

• fix compilesvstats.py svtypes

• updated papermillbase docker version build

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Co-authored-by: bshifaw bshifaw@broadinstitute.com
Co-authored-by: Steve Huang shuang@broadinstitute.org

lrp_4.0.11

Adding Base Image for Papermill Docker (#437)

• adding docker for papermill

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Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_4.0.10

Adding in all the work from the long-term Special Project Malaria branch (#440)

• Adding in all the work from the long-term Special Project Malaria branch

lrp_4.0.9

Added section on external contribution to development Readme (#435)

• Added section on external contribution

• Added links to repo site to main repo README.md

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Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_4.0.8

Merge pull request #428 from broadinstitute/tws_cleanup

repo cleanup