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Auto-Save Index Files Alongside BAMs #446

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Commits on Jan 10, 2023

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Commits on Jan 11, 2023

  1. Updated to GATK 4.3.0.0

    jonn-smith committed Jan 11, 2023
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  2. Added region annotation.

    jonn-smith committed Jan 11, 2023
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  3. Fixing vcf.gz typo

    jonn-smith committed Jan 11, 2023
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Commits on Jan 12, 2023

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Commits on Jan 14, 2023

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

    Some small optimizations too.
    SHuang-Broad authored and jonn-smith committed Jan 14, 2023
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  2. Autobump version 3.0.57 --> 3.0.58

    kvg authored and jonn-smith committed Jan 14, 2023
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  6. Change location of temp directory

    kvg authored and jonn-smith committed Jan 14, 2023
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  8. Performance improvements

    kvg authored and jonn-smith committed Jan 14, 2023
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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.
    kvg authored and jonn-smith committed Jan 14, 2023
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  16. Allocate more disk space

    kvg authored and jonn-smith committed Jan 14, 2023
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  18. Debugging

    kvg authored and jonn-smith committed Jan 14, 2023
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  19. More debugging

    kvg authored and jonn-smith committed Jan 14, 2023
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  20. Forgot to specify a disk size properly

    kvg authored and jonn-smith committed Jan 14, 2023
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  22. Try to resolve file corruption issue by separating the joint calling …

    …and conversion to .g.vcf.bgz steps
    kvg authored and jonn-smith committed Jan 14, 2023
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  23. Fixed bad temp dir specification

    kvg authored and jonn-smith committed Jan 14, 2023
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  26. Allow max cpus to be configurable

    kvg authored and jonn-smith committed Jan 14, 2023
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  27. Increase disk size request

    kvg authored and jonn-smith committed Jan 14, 2023
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  28. Temporary workflow to handle some issues arising from the LRJointCall…

    …GVCFs workflow
    kvg authored and jonn-smith committed Jan 14, 2023
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  29. Fixed a typo

    kvg authored and jonn-smith committed Jan 14, 2023
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  30. Added documentation

    kvg authored and jonn-smith committed Jan 14, 2023
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  31. Autobump version 3.0.58 --> 3.0.59

    kvg authored and jonn-smith committed Jan 14, 2023
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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
    jonn-smith committed Jan 14, 2023
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Commits on Jan 15, 2023

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

    …ead-pipelines into jts_kvg_sp_malaria
    kvg committed Jan 15, 2023
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  4. Reordering dockstore entries

    kvg committed Jan 15, 2023
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Commits on Jan 17, 2023

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  2. Fixing typos.

    jonn-smith committed Jan 17, 2023
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  5. Fixing disk space reqs.

    jonn-smith committed Jan 17, 2023
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Commits on Jan 23, 2023

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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.
    jonn-smith committed Feb 8, 2023
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Commits on Feb 9, 2023

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Commits on Feb 14, 2023

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  2. Fixing typos.

    jonn-smith committed Feb 14, 2023
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Commits on Feb 15, 2023

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  5. fixing typo.

    jonn-smith committed Feb 15, 2023
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Commits on Feb 16, 2023

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  3. Fixed file name.

    jonn-smith committed Feb 16, 2023
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Commits on Feb 27, 2023

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Commits on Feb 28, 2023

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Commits on Mar 1, 2023

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  3. Minor updates.

    jonn-smith committed Mar 1, 2023
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Commits on Mar 2, 2023

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  4. Fixed conda env sourcing.

    jonn-smith committed Mar 2, 2023
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  8. Fixing : -> . conversion.

    jonn-smith committed Mar 2, 2023
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Commits on Mar 7, 2023

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Commits on Mar 8, 2023

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Commits on Mar 12, 2023

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  2. Fixing typo

    jonn-smith committed Mar 12, 2023
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  4. Updated finalization info.

    jonn-smith committed Mar 12, 2023
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  5. Fixing issue.

    jonn-smith committed Mar 12, 2023
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Commits on Mar 23, 2023

  1. Fixing Barcode demo WDL.

    jonn-smith committed Mar 23, 2023
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Commits on May 11, 2023

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  2. Fixing typo.

    jonn-smith committed May 11, 2023
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Commits on Jun 7, 2023

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  4. Fixed a name conflict.

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

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  3. Fixing bug.

    jonn-smith committed Jul 4, 2023
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Commits on Jul 5, 2023

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Commits on Jul 10, 2023

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  2. Removing unused parameter.

    jonn-smith committed Jul 10, 2023
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  6. Fixing gzip issue.

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

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Commits on Jul 12, 2023

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  4. Adding debugging code.

    jonn-smith committed Jul 12, 2023
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Commits on Jul 13, 2023

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Commits on Jul 18, 2023

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Commits on Jul 20, 2023

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  5. Minor bugfix.

    jonn-smith committed Jul 20, 2023
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Commits on Aug 2, 2023

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Commits on Aug 9, 2023

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Commits on Aug 10, 2023

  1. Fixing CNN training task.

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

    jonn-smith committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. Added log messages.

    jonn-smith committed Aug 11, 2023
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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 committed Aug 18, 2023
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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 committed Sep 5, 2023
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Commits on Sep 6, 2023

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  4. Intermediate commit.

    jonn-smith committed Sep 6, 2023
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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 committed Sep 8, 2023
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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 committed Sep 8, 2023
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  3. Minor efficiency cleanup.

    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 committed Sep 8, 2023
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Commits on Sep 11, 2023

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Commits on Sep 12, 2023

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Commits on Sep 13, 2023

  1. Fxiing another typo/.

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

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  5. Additional debugging.

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

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

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Commits on Sep 18, 2023

  1. Fixed output file issue.

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

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Commits on Sep 21, 2023

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Commits on 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 committed Oct 8, 2023
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Commits on 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 committed Oct 9, 2023
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  6. Fixing typo.

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

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Commits on Nov 17, 2023

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Commits on Nov 27, 2023

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  3. Removed debugging code.

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

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  2. Renaming a wdl.

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

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

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Commits on Dec 2, 2023

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Commits on Dec 3, 2023

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Commits on Dec 4, 2023

  1. Fixing syntax error.

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

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Commits on Dec 6, 2023

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Commits on Dec 7, 2023

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  3. MAde BQSR optional.

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

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  11. Fixed a bug.

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

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Commits on Dec 14, 2023

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Commits on Jan 10, 2024

  1. Final cleanup commit.

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

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

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Commits on Apr 11, 2024

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  3. Update Utils.wdl

    - Local disk to SSD
    
    - samtools index -@ 2 ~{basename(prefix)}
    shadizaheri authored Apr 11, 2024
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