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Auto-Save Index Files Alongside BAMs #446

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Commits on Jan 10, 2023

  1. Added VQSR to SrWholeGenome and SRJointCallGVCFsWithGenomicsDB

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Commits on Jan 11, 2023

  1. Updated to GATK 4.3.0.0

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  2. Added region annotation.

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  3. Fixing vcf.gz typo

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  4. Fixed index extension error.

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  5. Updated more vcf.gz index names.

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Commits on Jan 12, 2023

  1. Fixed variant annotation task.

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Commits on Jan 14, 2023

  1. Terra changed where submissions go (now at gs://<bucket>/submissions/) 

    Some small optimizations too.
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  2. Autobump version 3.0.57 --> 3.0.58

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  3. Workflow to perform joint calling on gVCFs with GLNexus

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  4. Workflow for joint-calling gVCFs with GLNexus

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  5. Increased size of disk to store intermediate files

    @kvg @jonn-smith
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  6. Change location of temp directory

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  7. Separate joint calling from bgzipping and indexing for better restart… 

    …ability.
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  8. Performance improvements

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  9. Revert those changes because the amount of disk space we need is actu… 

    …ally too large to benefit from Steve's ComputeAllowedLocalSSD optimization.
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  10. Now optimized to use multiple high-performance disks

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  11. Create a Hail MatrixTable of the joint-called VCF

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  12. Some reorganization that will hopefully improve call-caching.

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  13. Some simplifications to Hail MT delocalization

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  14. Changed some variable names for consistency

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  15. Temporary workflow to convert an existing GVCF to a Hail MatrixTable

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  16. Allocate more disk space

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  17. Allow optional specification of a reference sequence for Hail

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  18. Debugging

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  19. More debugging

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  20. Forgot to specify a disk size properly

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  21. Custom reference sequence usage needs to be specified in the hl.impor… 

    …t_vcf call
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  22. Try to resolve file corruption issue by separating the joint calling … 

    …and conversion to .g.vcf.bgz steps
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  23. Fixed bad temp dir specification

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  24. A contig-parallelized joint-calling workflow

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  25. Forgot to surround optional num_cpus in select_first()

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  26. Allow max cpus to be configurable

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  27. Increase disk size request

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  28. Temporary workflow to handle some issues arising from the LRJointCall… 

    …GVCFs workflow
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  29. Fixed a typo

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  30. Added documentation

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  31. Autobump version 3.0.58 --> 3.0.59

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  32. Added workflow to convert a BAM file to fastq files

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  33. Many updates for short read Malaria processing. 

    - Added SRFlowcell.wdl, SRWholeGenome.wdl
- Added SRJointGenotyping.wdl, LRJointCallGVCFsWithGenomicsDB.wdl
- Updated `sr-utils` docker image
- Workflow to index a BAM file

- Whole genome processing pipeline for short read data

- Added short read whole genome pipeline to Dockstore

- Added start to workflows to do GCNV calling.

- Added LRJointCallGVCFsWithGenomicsDB to dockstore.
- Removed downstream calls to `nanoplot` in SRWholeGenome
- Added hail matrix table output to LRJointCallGVCFsWithGenomicsDB
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  34. Fixed genome name in Hail MT

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Commits on Jan 15, 2023

  1. Added workflow to create a Zarr store

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  2. Merge branch 'jts_kvg_sp_malaria' of github.com:broadinstitute/long-r… 

    …ead-pipelines into jts_kvg_sp_malaria
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  3. Register Zarr store workflow in Dockstore

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  4. Reordering dockstore entries

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Commits on Jan 17, 2023

  1. Adding in temporary WDL to work around dockstore.

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  2. Fixing typos.

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  3. Updating disk space required for ImportGVCFs

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  4. Fixing disk space issue with genomicsDB.

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  5. Fixing disk space reqs.

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  6. Fixed woeful byte -> GB conversion error.

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  7. Fixing dupe entries in .dockstore.yml

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  8. Adjusted disk size due to tar in the command block of ImportGVCFs

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  9. Removed preemption from ImportGVCFs

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  10. Updated calls to have 0 preemptable attempts (for now).

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  11. Attempt to fix read_int issue.

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Commits on Jan 23, 2023

  1. Fixed issue with disk size in Joint Calling.

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Commits on Feb 8, 2023

  1. Minor updates to variant / joint calling. 

    - Joint calling now is no longer preemptible.
- added `--annotate-with-num-discovered-alleles` flag to
  HaplotypeCaller.
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  2. Adding in diagram of lrma-sp-malaria pipeline.

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Commits on Feb 9, 2023

  1. Minor change to legacy monitoring script.

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Commits on Feb 14, 2023

  1. Added BenchmarkVCFs and instrumentation to other tasks.

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  2. Fixing typos.

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Commits on Feb 15, 2023

  1. Adding BenchmarkVCFs to dockstore.

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  2. Fixing output name in SRWholeGenome.wdl

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  3. Minor changes to BenchmarkVCFs

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  4. Adding support for viewing reads in the auto-generated IGV sessions.

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  5. fixing typo.

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Commits on Feb 16, 2023

  1. Fixed formatting and problem with IGV xml generation.

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  2. Added CompareVcfBenchmarks.wdl.

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  3. Fixed file name.

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  4. Changing default for gc plots.

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Commits on Feb 27, 2023

  1. Adding resources.log to outputs for monitored tasks.

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Commits on Feb 28, 2023

  1. Added instrumentation for the rest of the WDLs to check resources.

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  2. Adding in docker image for malaria work.

    @jonn-smith
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  3. Fixing requirements for barcode script.

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  4. Cleaned up the barcode script a little.

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Commits on Mar 1, 2023

  1. Updated barcode script to handle csv/tsv input.

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  2. Now it actually works for CSVs/TSVs.

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  3. Minor updates.

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  4. Fixed ingest of new barcode def TSV.

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Commits on Mar 2, 2023

  1. Adding in WDL for P. falciparum barcode panel processing.

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  2. Adding PanelProcessMalariaBarcodesForRh.wdl to dockstore.

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  3. Adding some tests for python versioning and conda env.

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  4. Fixed conda env sourcing.

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  5. Fixed orientation of input tsv.

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  6. Changing Multi/Poly column name to Terra convention.

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  7. Fixing parsing issue with ISO3 field.

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  8. Fixing : -> . conversion.

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  9. Adding outputs to the WDL.

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  10. Fixing outputs in the workflow.

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Commits on Mar 7, 2023

  1. Fixed bug in hail.wdl, updated docs for Panel wdl.

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Commits on Mar 8, 2023

  1. Adding in images for better documentation in the barcode workspace

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Commits on Mar 12, 2023

  1. Added in renaming the sample to the new sample name in SRWholeGenome.

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  2. Fixing typo

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  3. Adding indexing to Rename task.

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  4. Updated finalization info.

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  5. Fixing issue.

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  6. Fixing sample name in other haplotypecaller files.

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Commits on Mar 23, 2023

  1. Fixing Barcode demo WDL.

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  2. Adding ProcessMalariaBarcodesDemo to dockstore.

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  3. Removed finalization inputs.

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Commits on May 11, 2023

  1. Added ability to use sites-only VCFs as truth.=

    @jonn-smith
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  2. Fixing typo.

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    jonn-smith committed May 11, 2023
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  3. Fixing args with ALT sample mode.

    @jonn-smith
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  4. Fixing a bug in final stats counting

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Commits on Jun 7, 2023

  1. Added step to actually remove filtered variants.

    @jonn-smith
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  2. Fixed VQSR filtered output

    @jonn-smith
    jonn-smith committed Jun 7, 2023
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  3. Fixed typo in finalization.

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  4. Fixed a name conflict.

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    jonn-smith committed Jun 7, 2023
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Commits on Jul 1, 2023

  1. Removing allele-specific annotations.

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Commits on Jul 2, 2023

  1. Exposed more recalibration inputs.

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  2. Fixing type issue with VQSR priors.

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Commits on Jul 3, 2023

  1. Fixing long read joint calling wdl.

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Commits on Jul 4, 2023

  1. Fixed modified joint calling to be faster.

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  2. Adding SRJointCallGVCFsWithGenomicsDB to dockstore.

    @jonn-smith
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  3. Fixing bug.

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Commits on Jul 5, 2023

  1. Parallelized the joint call. Added functional annotation.

    @jonn-smith
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  2. Fixing issue with reblock GVCFs

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Commits on Jul 6, 2023

  1. Adding Zarr conversion into SR Joint Calling WDL.

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  2. Removing automatic Zarr conversion

    @jonn-smith
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Commits on Jul 10, 2023

  1. Fixed issue with VQSR in SRJointCallGVCFsWithGenomicsDB.wdl

    @jonn-smith
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  2. Removing unused parameter.

    @jonn-smith
    jonn-smith committed Jul 10, 2023
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  3. Fixed a bug in GatherVCFsCloud

    @jonn-smith
    jonn-smith committed Jul 10, 2023
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  4. Fixed typo in ApplyVQSR task.

    @jonn-smith
    jonn-smith committed Jul 10, 2023
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  5. Fixing vcf extension for some outputs.

    @jonn-smith
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  6. Fixing gzip issue.

    @jonn-smith
    jonn-smith committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. Fixed bgzip of SNPEff output.

    @jonn-smith
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  2. Adding functional annotation docker.

    @jonn-smith
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  3. Moving snpEff to a new docker image.

    @jonn-smith
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Commits on Jul 12, 2023

  1. Another fix for the bgzip issue in functional annotation.

    @jonn-smith
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  2. Updated GatherVCFs task to emit vcf.gz files.

    @jonn-smith
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  3. Removed explicit tabix index from GatherVCFsCloud.

    @jonn-smith
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  4. Adding debugging code.

    @jonn-smith
    jonn-smith committed Jul 12, 2023
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  5. Added back in the tabix indexing.

    @jonn-smith
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  6. Fixing elusive typo in outputs for GatherVCFs

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Commits on Jul 13, 2023

  1. Added output for annotated VCF.

    @jonn-smith
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  2. Fixed outputs for SRJointCallGVCFsWithGenomicsDB.wdl

    @jonn-smith
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Commits on Jul 18, 2023

  1. Fixing issue in SRWholeGenome caused by previous commit.

    @jonn-smith
    jonn-smith committed Jul 18, 2023
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Commits on Jul 20, 2023

  1. Fixing critical bug in SRUtils::Bam2Fq

    @jonn-smith
    jonn-smith committed Jul 20, 2023
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  2. Fixed corner case in Finalize::FinalizeToDir

    @jonn-smith
    jonn-smith committed Jul 20, 2023
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  3. Whitespace change to make dockstore register changes.

    @jonn-smith
    jonn-smith committed Jul 20, 2023
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  4. Fixing issue with bash string comparisons in Finalize::FinalizeToDir

    @jonn-smith
    jonn-smith committed Jul 20, 2023
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  5. Minor bugfix.

    @jonn-smith
    jonn-smith committed Jul 20, 2023
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Commits on Aug 1, 2023

  1. Added wdl to train CNNScoreVariants.

    @jonn-smith
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  2. Added wdl to train CNN filters.

    @jonn-smith
    jonn-smith committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. Added in more memory for MarkDuplicates.

    @jonn-smith
    jonn-smith committed Aug 2, 2023
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  2. Fixing memory for MarkDuplicates.

    @jonn-smith
    jonn-smith committed Aug 2, 2023
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  3. Giving more headroom for OS processes.

    @jonn-smith
    jonn-smith committed Aug 2, 2023
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Commits on Aug 9, 2023

  1. Fixed disk space in Create2DReadTensors

    @jonn-smith
    jonn-smith committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. Fixing CNN training task.

    @jonn-smith
    jonn-smith committed Aug 10, 2023
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  2. Fixing another typo.

    @jonn-smith
    jonn-smith committed Aug 10, 2023
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  3. Removing preemptible from CNN Training WDL.

    @jonn-smith
    jonn-smith committed Aug 10, 2023
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  4. Provisioned GPUs for TrainCNN.

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Commits on Aug 11, 2023

  1. Added log messages.

    @jonn-smith
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Commits on Aug 18, 2023

  1. Updated CNN model training and haplotypecaller parameters. 

    - Exposed CNN model training parameters in the WDLs.
- Set `HaplotypeCaller` to use the AVX accelerated Smith-Waterman
  library if it is possible on the executing machine.
    @jonn-smith
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Commits on Sep 5, 2023

  1. Multiple updates. 

    - Added some NaN checking in TrainCnnFilters.wdl
- Updated SRWholeGenome and HaplotypeCaller to include an option to use
  pileup mode.
    @jonn-smith
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Commits on Sep 6, 2023

  1. Added task to compute fingerprint of a bam file.

    @jonn-smith
    jonn-smith committed Sep 6, 2023
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  2. Added task for ExtractVariantAnnotations

    @jonn-smith
    jonn-smith committed Sep 6, 2023
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  3. Added task for TrainVariantAnnotationsModel

    @jonn-smith
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  4. Intermediate commit.

    @jonn-smith
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Commits on Sep 8, 2023

  1. Updates for VETS integration and file outputs. 

    - Updated workflows to use finalized files as outputs instead of files in the working directories.
- Fixed validation error in `LRJointCallGVCFsWithGenomicsDB.wdl`.
- Updated `SRJointCallGVCFsWithGenomicsDB.wdl` to use VETS instead of VQSR.
    @jonn-smith
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  2. Updates for barcoding. 

    - Added fingerprinting / barcode task, `ExtractFingerprintAndBarcode`, to `VariantUtils.wdl`.
- Added call to `ExtractFingerprintAndBarcode` in `SRWholeGenome.wdl`.
- Updated version of sr-utils to latest in `SRUtils::BwaMem2`.
    @jonn-smith
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  3. Minor efficiency cleanup.

    @jonn-smith
    jonn-smith committed Sep 8, 2023
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  4. Updates to functional annotation. 

    - Now FunctionalAnnotation::FunctionallyAnnotateVariants natively
  produces a VCF Index.
- `SRJointCallGVCFsWithGenomicsDB` and `ONTPfTypeDrugResistanceMarkers`
  now use the new natively-produced VCF index and do not re-index the
  file.
- `ONTPfTypeDrugResistanceMarkers` can now optionally skip to the
  `CallDrugResistanceMutations` step if the input file is already
  functionally annotated.
    @jonn-smith
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Commits on Sep 11, 2023

  1. Added more snpEff outputs to SRJointCallGVCFsWithGenomicsDB

    @jonn-smith
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Commits on Sep 12, 2023

  1. Fixing the outputs for merge vcfs.

    @jonn-smith
    jonn-smith committed Sep 12, 2023
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  2. Fixing bug in WDL for ExtractVariantAnnotations and `ScoreVariantAn… 

    …notations`.
    @jonn-smith
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Commits on Sep 13, 2023

  1. Fxiing another typo/.

    @jonn-smith
    jonn-smith committed Sep 13, 2023
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  2. Fixed a copy/paste error for memory configuration in a few tasks.

    @jonn-smith
    jonn-smith committed Sep 13, 2023
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  3. Fixing typo in argument for ScoreVariantAnnotations

    @jonn-smith
    jonn-smith committed Sep 13, 2023
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  4. Fixed typo in ScoreVariantAnnotations and ExtractVariantAnnotations.

    @jonn-smith
    jonn-smith committed Sep 13, 2023
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Commits on Sep 14, 2023

  1. Adding some debugging for outputs.

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  2. Fixing outputs for TrainVariantAnnotationsModel

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  3. Fixing the same output file issue.

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  4. Updated ScoreVariantAnnotations with some debugging.

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  5. Additional debugging.

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  6. Fixing typo in SRWholeGenome for VETS.

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  7. Fixing yet another typo in SRWholeGenome

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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  8. Fixed another issue.

    @jonn-smith
    jonn-smith committed Sep 14, 2023
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Commits on Sep 15, 2023

  1. Fixing barcode extraction wdl.

    @jonn-smith
    jonn-smith committed Sep 15, 2023
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  2. Updated output type of barcode to be String instead of File.

    @jonn-smith
    jonn-smith committed Sep 15, 2023
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  3. Removing separate log file for gatk in VETS tasks.

    @jonn-smith
    jonn-smith committed Sep 15, 2023
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Commits on Sep 18, 2023

  1. Fixed output file issue.

    @jonn-smith
    jonn-smith committed Sep 18, 2023
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  2. Fixing issue in joint calling workflow.

    @jonn-smith
    jonn-smith committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. Added flag to SRWholeGenome to indicate data has been processed.

    @jonn-smith
    jonn-smith committed Sep 19, 2023
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  2. Changed snpEff results folder name

    @jonn-smith
    jonn-smith committed Sep 19, 2023
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  3. Added Workflow to extract single-organism contaminants.

    @jonn-smith
    jonn-smith committed Sep 19, 2023
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  4. Fixed outputs for RemoveSingleOrganismContaminationto be finalized.

    @jonn-smith
    jonn-smith committed Sep 19, 2023
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  5. Connected RemoveSingleOrganismContamination in SRFlowcell

    @jonn-smith
    jonn-smith committed Sep 19, 2023
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Commits on Sep 21, 2023

  1. Increasing the memory for contamination alignment

    @jonn-smith
    jonn-smith committed Sep 21, 2023
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  2. Adding missing sort step to read decontamination workflow.

    @jonn-smith
    jonn-smith committed Sep 21, 2023
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  3. Fixed RemoveSingleOrganismContamination. Minor change to ReblockGVCFs

    @jonn-smith
    jonn-smith committed Sep 21, 2023
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  4. Fixing issue in SRFlowcell caused by other chantges.

    @jonn-smith
    jonn-smith committed Sep 21, 2023
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Commits on Sep 25, 2023

  1. Removed decontamination task. Added AlignedMetrics.

    @jonn-smith
    jonn-smith committed Sep 25, 2023
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Commits on Oct 8, 2023

  1. Added WDL to extract reads from amplicon regions. 

    Added `ExtractRegionsFromBam.wdl`
Added task: `Utils::GetReadsInBedfileRegions`
Minor comments added to `VariantUtils::ExtractFingerprintAndBarcode`
    @jonn-smith
    jonn-smith committed Oct 8, 2023
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Commits on Oct 9, 2023

  1. Added new diagram of high-level view of pipeline.

    @jonn-smith
    jonn-smith committed Oct 9, 2023
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  2. Adding in workspace markdown documentation.

    @jonn-smith
    jonn-smith committed Oct 9, 2023
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  3. Updated workspace markdown doc.

    @jonn-smith
    jonn-smith committed Oct 9, 2023
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  4. Updated dockstore; Added PfalciparumDrugResistanceSummary.wdl 

    - Added `PfalciparumDrugResistanceSummary.wdl`
- Added `PfalciparumDrugResistanceSummary.wdl` and
  `ExtractRegionsFromBam.wdl` to `.dockstore.yml`
- parameter_meta change in ExtractRegionsFromBam.wdl
    @jonn-smith
    jonn-smith committed Oct 9, 2023
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  5. Fixing bug in PfalciparumDrugResistanceSummary.wdl

    @jonn-smith
    jonn-smith committed Oct 9, 2023
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  6. Fixing typo.

    @jonn-smith
    jonn-smith committed Oct 9, 2023
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Commits on Nov 13, 2023

  1. Adding docker file and make file for Karamoko Niare's pipeline.

    @jonn-smith
    jonn-smith committed Nov 13, 2023
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  2. Fixed bugs in sr-malaria-niare-pipeline dockerfile.

    @jonn-smith
    jonn-smith committed Nov 13, 2023
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Commits on Nov 17, 2023

  1. Exposed het rate parameters.

    @jonn-smith
    jonn-smith committed Nov 17, 2023
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Commits on Nov 27, 2023

  1. Adding debug info to BenchmarkVCFs.wdl

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    jonn-smith committed Nov 27, 2023
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  2. Commenting out debugging code.

    @jonn-smith
    jonn-smith committed Nov 27, 2023
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  3. Removed debugging code.

    @jonn-smith
    jonn-smith committed Nov 27, 2023
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Commits on Nov 30, 2023

  1. Added in WDLs to reproduce Niare et al. GATK4 pipeline.

    @jonn-smith
    jonn-smith committed Nov 30, 2023
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  2. Renaming a wdl.

    @jonn-smith
    jonn-smith committed Nov 30, 2023
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  3. Adding Niare et al. WDLs to dockstore.

    @jonn-smith
    jonn-smith committed Nov 30, 2023
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  4. Removed manual monitoring instrumentation.

    @jonn-smith
    jonn-smith committed Nov 30, 2023
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  5. Fixing typo.

    @jonn-smith
    jonn-smith committed Nov 30, 2023
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Commits on Dec 1, 2023

  1. Fixing bugs in sr-malaria-niare-pipeline dockerfile.

    @jonn-smith
    jonn-smith committed Dec 1, 2023
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  2. Cleaned up docker image for niare paper.

    @jonn-smith
    jonn-smith committed Dec 1, 2023
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Commits on Dec 2, 2023

  1. increasing resources for niare hc

    @jonn-smith
    jonn-smith committed Dec 2, 2023
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  2. Fixing missing parameters in niare wdls

    @jonn-smith
    jonn-smith committed Dec 2, 2023
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Commits on Dec 3, 2023

  1. Removed R script from niare haplotypecaller.

    @jonn-smith
    jonn-smith committed Dec 3, 2023
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  2. Fixing outputs in Niare VETS workflow.

    @jonn-smith
    jonn-smith committed Dec 3, 2023
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  3. Removed R script output for niare vqsr

    @jonn-smith
    jonn-smith committed Dec 3, 2023
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Commits on Dec 4, 2023

  1. Fixing syntax error.

    @jonn-smith
    jonn-smith committed Dec 4, 2023
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  2. Fixing logic error in Niare VQSR pipeline.

    @jonn-smith
    jonn-smith committed Dec 4, 2023
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  3. Fixing issue where variants in Niare pipeline would be duplicated.

    @jonn-smith
    jonn-smith committed Dec 4, 2023
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  4. Fixing bad input in Niare workflows.

    @jonn-smith
    jonn-smith committed Dec 4, 2023
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Commits on Dec 5, 2023

  1. Fixing file / string mixup in Niare HC.

    @jonn-smith
    jonn-smith committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. Fixing mito contig name in Niare VQSR workflow.

    @jonn-smith
    jonn-smith committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. Removing contig sharding from VQSR in niare to fix variance issue.

    @jonn-smith
    jonn-smith committed Dec 7, 2023
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  2. Fixing yet another issue in the vqsr stuff.

    @jonn-smith
    jonn-smith committed Dec 7, 2023
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  3. MAde BQSR optional.

    @jonn-smith
    jonn-smith committed Dec 7, 2023
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Commits on Dec 12, 2023

  1. Adding new WDL for expanded drug resistance markers.

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  2. Adding ExpandedDrugResistanceMarkerExtraction to dockstore.

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  3. Fixed issue in ExpandedDrugResistanceMarkerExtraction.wdl

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  4. Adding genotype info to drug resistance extraction.

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  5. Adding ExpandedDrugResistanceMarkerAggregation.wdl

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  6. Fixing het value in aggregation table.

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  7. Changing output format for ExpandedDrugResistanceMarkerExtraction.wdl

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  8. Updating format for ExpandedDrugResistanceMarkerExtraction.wdl again

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  9. Fixed ExpandedDrugResistanceMarkerAggregation.wdl for new formats.

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  10. Fixing bug in ExpandedDrugResistanceMarkerAggregation.wdl

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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  11. Fixed a bug.

    @jonn-smith
    jonn-smith committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. Fixing another bug in ExpandedDrugResistanceMarkerAggregation.wdl

    @jonn-smith
    jonn-smith committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. Now expanded drug reports contain synonymous mutations as well.

    @jonn-smith
    jonn-smith committed Dec 14, 2023
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  2. Changed how file localization happens in ExpandedDrugResistanceMarker… 

    …Aggregation.wdl
    @jonn-smith
    jonn-smith committed Dec 14, 2023
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  3. Fixing a typo in ExpandedDrugResistanceMarkerAggregation.wdl

    @jonn-smith
    jonn-smith committed Dec 14, 2023
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  4. Fixing trailing tab character.

    @jonn-smith
    jonn-smith committed Dec 14, 2023
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Commits on Jan 10, 2024

  1. Final cleanup commit.

    @jonn-smith
    jonn-smith committed Jan 10, 2024
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  2. Deprecating this branch.

    @jonn-smith
    jonn-smith committed Jan 10, 2024
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Commits on Feb 28, 2024

  1. Fixed an incorrect filename specification

    @kvg
    kvg committed Feb 28, 2024
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Commits on Apr 11, 2024

  1. Streamlined BAM Index File Storage

    @shadizaheri
    shadizaheri committed Apr 11, 2024
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  2. Streamlined BAM Index File Storage (added the modified SRIndexBam wor… 

    …kflow)
    @shadizaheri
    shadizaheri committed Apr 11, 2024
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  3. Update Utils.wdl 

    - Local disk to SSD

- samtools index -@ 2 ~{basename(prefix)}
    @shadizaheri
    shadizaheri committed Apr 11, 2024
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