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Merging development branch from Malaria project - decontamination, pipelines for organisms with no variant truth set, etc. #451

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Merging development branch from Malaria project - decontamination, pipelines for organisms with no variant truth set, etc. #451

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Commits on Jan 30, 2024

  1. Update AlignedMetrics.wdl to expose runtime_attr_override

    @brosula
    brosula authored Jan 30, 2024
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  2. Memory bump to ReadMetrics task in AlignedMetrics.wdl

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Commits on Feb 5, 2024

  1. Create SRDownsampleBam

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  2. Update .dockstore.yml to include SRDownsampleBam

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  3. Add SRDownsampleBam.wdl

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  4. Update .dockstore.yml to include SRDownsampleBam.wdl

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  5. include Finalize in SRDownsampleBam.wdl

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  6. Update .dockstore.yml

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  7. add bam size to SRDownsampleBam.wdl

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  8. rename conflicting variables in SRDownsampleBam.wdl

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Commits on Feb 6, 2024

  1. Update paths in SRDownsampleBam.wdl

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  2. Update paths in SRIndexBam.wdl

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  3. Update paths in SRIndexBam.wdl

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  4. Update parameter typo in SRIndexBam.wdl

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Commits on Apr 1, 2024

  1. Added Bowtie2 alignment functionality to SRUtils.wdl

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  2. Added Bowtie2 as an option for decontamination

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    brosula committed Apr 1, 2024
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  3. Dockerfile for bowtie2

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    brosula committed Apr 1, 2024
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  4. Added Bowtie2 as an option for decontamination

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  5. Added Bowtie2 decontamination to SRFlowcell

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  6. Added Bowtie2 decontamination to SRFlowcell

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Commits on Apr 2, 2024

  1. Correct ref_basename type to String

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    brosula committed Apr 2, 2024
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  2. removed if statement in SRFlowcell

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    brosula committed Apr 2, 2024
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  3. corrected directory naming for bowtie2

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    brosula committed Apr 2, 2024
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  4. Change samtools view command

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    brosula committed Apr 2, 2024
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Commits on Apr 3, 2024

  1. Update bowtie2 rg-id

    @brosula
    brosula committed Apr 3, 2024
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  2. Output sam for debugging

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    brosula committed Apr 3, 2024
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  3. Redefine read group according to bowtie2 specs

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    brosula committed Apr 3, 2024
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  4. read in optional inputs correctly to Bowtie2

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    brosula committed Apr 3, 2024
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  5. corrected bowtie2 read group strings

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    brosula committed Apr 3, 2024
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  6. Added SRFlowcellDecontaminate.wdl workflow

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  7. Add SRFlowcellDecontaminate to dockstore

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    brosula committed Apr 3, 2024
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  8. Update bowtie2 command

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    brosula committed Apr 3, 2024
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  9. Update bowtie2 command

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    brosula committed Apr 3, 2024
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Commits on Apr 16, 2024

  1. 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.
    @jonn-smith
    jonn-smith committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. Removed hard filtered output file.

    @jonn-smith
    jonn-smith committed Apr 17, 2024
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  2. Updating all GATK 4.3 tasks to GATK 4.5

    @jonn-smith
    jonn-smith committed Apr 17, 2024
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Commits on Apr 18, 2024

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

    @jonn-smith
    jonn-smith committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. Added a runtime_attr override for HaplotypeCaller subworkflow.

    @jonn-smith
    jonn-smith committed Apr 19, 2024
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  2. Update Utils.wdl 

    Modified the disks from " LOCAL" to " SSD"
    @shadizaheri
    shadizaheri authored Apr 19, 2024
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Commits on Apr 22, 2024

  1. Updating tasks to use SSD rather than LOCAL disk.

    @jonn-smith
    jonn-smith committed Apr 22, 2024
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  2. Merge remote-tracking branch 'origin/jts_updates_to_malaria_for_joint… 

    …_calling' into rrb_malaria_from_main
    @brosula
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  3. Merge _Bootstrap wdls into rrb_malaria_from_main branch, add standalo… 

    …ne SRReblockGVCFs wdl
    @brosula
    brosula committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. Correct arguments of HaplotypeCallerBootstrap.wdl

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    brosula committed Apr 23, 2024
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  2. Add size reduction reporting to SRReblockGVCFs

    @brosula
    brosula committed Apr 23, 2024
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  3. Add ref_map_file to SRReblockGVCFs

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    brosula committed Apr 23, 2024
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  4. Finalize files to gcs path in SRReblockGVCFs

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    brosula committed Apr 23, 2024
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  5. Remove prefix option in favor of participant_name

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  6. Remove prefix option in favor of participant_name

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Commits on Apr 26, 2024

  1. Update HaplotypeCallerBootstrap.wdl to GATK v4.5.0

    @brosula
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Commits on May 2, 2024

  1. Update containers in HaplotypeCaller to recent nightly snapshot of GATK4

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  2. Update to GATK 4.5

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Commits on May 6, 2024

  1. Add contaminated bam/metrics to SRFlowcell output

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Commits on May 14, 2024

  1. Add workflows/tasks to extract genome-wide depth from mosdepth and me… 

    …rging vcfs with diff. samples
    @brosula
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  2. correct spelling in .dockstore.yml

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    brosula committed May 14, 2024
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  3. Localize contig_files instead

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  4. Correct reference to localized file in ExtractCoverageFromMosDepth.wdl

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  5. Use Mosdepth to calculate WGS coverage statistics (derived from PMICP… 

    …_Main branch)
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Commits on May 15, 2024

  1. Add error catch for empty string produced from checking threshold

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  2. Use mosdepth and samtools coverage tools

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  3. Remove ref_map_file for ExtractCoverageStats.wdl

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  4. Correct calculation to account for files with low threshold

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    brosula committed May 15, 2024
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  5. Correct awk script

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    brosula committed May 15, 2024
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  6. Correct samtools command

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Commits on May 18, 2024

  1. Make gcs_out_root_dir optional (prepare for merge with main)

    @brosula
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  2. Merge remote-tracking branch 'origin/main' into rrb_malaria_from_main

    @brosula
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  3. Correct for optional gcs_out_root_dir in SRJointCallGVCFsWithGenomics… 

    …DBBootstrap

( no sharding of snpeff_db implemented )
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Commits on May 25, 2024

  1. Change handling of optional decontamination/contamination outputs

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    brosula committed May 25, 2024
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Commits on May 28, 2024

  1. Specify intervals for manual sharding in SRJointCallGVCFsWithGenomicsDB

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    brosula committed May 28, 2024
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Commits on May 29, 2024

  1. Correct index for scattering in SRJointCallGVCFsWithGenomicsDB

    @brosula
    brosula committed May 29, 2024
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  2. Scatter contig_2 with manual indexes

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    brosula committed May 29, 2024
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  3. Add DownloadFromFTP to Dockstore

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    brosula committed May 29, 2024
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Commits on May 31, 2024

  1. Add option to turn off scattering for MosDepth

    @brosula
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  2. Add raw_chr_intervals for SRFlowcell keyfile

    @brosula
    brosula committed May 31, 2024
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  3. Surface per_chr_metrics Boolean in SRFlowcell

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Commits on Jun 26, 2024

  1. Update SRWholeGenomeBootstrap.wdl to default to False for pileup dete… 

    …ction
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    brosula authored Jun 26, 2024
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Commits on Oct 16, 2024

  1. Update MosDepthWGSAtThreshold to report correct metrics 

    Report the correct coverage metric when given a BED file.
    @brosula
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  2. Update MosDepth to report whole genome coverage with BED file

    @brosula
    brosula authored Oct 16, 2024
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