Releases · broadinstitute/long-read-pipelines

06 Aug 17:03

github-actions

4.0.19

ec0f5b5

lrp_4.0.19

Cleaned up short read workflows, minor feature additions (#461)

Added docker image and WDL to backup workspaces.
Added util-malaria-coi docker image.
Fixed bug in SRFlowcell that preferentially pulled the existing aligned bam rather than the merged aligned bam.
Cleaned up redundant / unnecessary inputs and outputs from SRWholeGenome.wdl
Enabled SRWholeGenome.wdl and HaplotypeCaller.wdl to use an interval_list to call variants in subsets of the genome.
Renamed ONTPfTypeDrugResistanceMarkers.wdl to PfalciparumTypeDrugResistanceMarkers.wdl.
Renamed ONTPfHrp2Hrp3Status.wdl to PfalciparumHrp2Hrp3Status.wdl
PfalciparumDrugResistanceSummary.wdl now produces individual drug resistances/sensitivites as additional outputs.
PfalciparumDrugResistanceSummary.wdl is now deprecated.
PfalciparumDrugResistanceMarkers.wdl now produces drug resistances/sensitivites as well as the summary file. This deprecates PfalciparumDrugResistanceSummary.wdl.
Added PfalciparumPolygenomicityBarcodeEstimate.wdl to estimate CoI based on the 24 SNP molecular barcode.
Cleaned up some outputs in SRJointCallGVCFsWithGenomicsDB.wdl.
Added flag for dangling end recovery to HaplotypeCaller.wdl.
Minor fixes for MiniWDL style suggestions (TrainCnnFilters.wdl, LRCNVs.wdl, AlignedMetrics.wdl, FastQC.wdl, SRUtils.wdl, Utils.wdl, VariantUtils.wdl, SRJointGenotyping.wdl, NanoPlot.wdl, Pf_Niare_HaplotypeCaller.wdl)

Assets 2

27 Jun 16:04

github-actions

4.0.18

11c576a

lrp_4.0.18

Reworked SRJointGenotyping sharding to be configurable at runtime. (#455)

Sharding now splits the VCF files into chunks by number of bp. This
allows for wider sharding / better scalability for large callsets.
By default the behavior is to shard by contig - this is controlled by
setting the number of bp per shard to be very large (999999999). If
the number of bp per shard is larger than the contig size, the whole
contig is used.
Changed MakeSitesOnlyVCF task to use bcftools.
Updated joint call WDL to accept interval lists.

Assets 2

15 May 18:36

github-actions

4.0.17

bce6165

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

Assets 2

08 May 18:57

github-actions

4.0.16

7c8cfd7

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

Assets 2

03 May 02:44

github-actions

4.0.15

8656736

lrp_4.0.15

make submissions folder deletion better (#445)

make submissions folder deletion better

Assets 2

24 Apr 15:04

github-actions

4.0.14

3168f8d

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.