.pullapprove.yml

---
version: 3

  # DO NOT EDIT THIS FILE DIRECTLY!!!
# To edit the pullapprove.yml file, edit the pullapprove_template.yml file or the scripts/process.sh script instead.
# Top level wdls for each pipeline are defined in the scripts/process.sh script.
# All other content in this file can be found in pullapprove_template.yml.
# After editing, run the process.sh script from within the scripts directory to update this file based on your changes.
# Changing this file directly will result in your changes being overwritten the next time process.sh is run.


pullapprove_conditions:
  - condition: "'WIP' not in title"
    unmet_status: pending
    explanation: "Work in progress"
  - condition: "'WIP' not in labels"
    unmet_status: pending
    explanation: "Work in progress"
  - condition: "'do not merge' not in labels"
    unmet_status: failure
    explanation: "Do Not Merge"


groups:
  # Reviews from 2 developers are required for any PR
  developers:
    reviews:
      required: 2
      request: 0  # number of review requests sent at a time
    reviewers:
      teams:
        - dsde-pipelines-developers

  # Reviews from scientific owners:
  # - will not be required if the 'eng-only' label is applied

  scientific_owners_arrays:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl' in files or
        'pipelines/broad/arrays/single_sample/Arrays.wdl' in files or
        'pipelines/broad/arrays/validate_chip/ValidateChip.wdl' in files or
        'pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl' in files or
        'tasks/broad/IlluminaGenotypingArrayTasks.wdl' in files or
        'tasks/broad/InternalArraysTasks.wdl' in files or
        'tasks/broad/InternalTasks.wdl' in files or
        'tasks/broad/Utilities.wdl' in files or
        'verification/VerifyArrays.wdl' in files or
        'verification/VerifyIlluminaGenotypingArray.wdl' in files or
        'verification/VerifyMetrics.wdl' in files or
        'verification/VerifyMultiSampleArrays.wdl' in files or
        'verification/VerifyTasks.wdl' in files or
        'verification/VerifyValidateChip.wdl' in files or
        'pipelines/broad/arrays/imputation' in files or
        'pipelines/broad/arrays/multi_sample' in files or
        'pipelines/broad/arrays/single_sample' in files or
        'pipelines/broad/arrays/validate_chip' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 1
      request_order: given
    reviewers:
      users:
        - gbggrant # George Grant

  scientific_owners_gdc_pipeline:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl' in files or
        'tasks/broad/CheckContaminationSomatic.wdl' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDC.png' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.options.json' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/README.md' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/biobambam2' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/bwa' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/input_files' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/samtools_nio' in files or
        'pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/test_inputs' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 1
      request_order: given
    reviewers:
      users:
        - chipstewart # Chip Stewart

  scientific_owners_cram_to_unmapped_bam:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.changelog.md' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.options.json' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/input_files' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/test_inputs' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 1
      request_order: given
    reviewers:
      users:
        - kachulis # Chris Kachulis

  scientific_owners_germline_single_sample:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl' in files or
        'pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl' in files or
        'pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl' in files or
        'pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl' in files or
        'pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl' in files or
        'pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl' in files or
        'structs/dna_seq/DNASeqStructs.wdl' in files or
        'tasks/broad/AggregatedBamQC.wdl' in files or
        'tasks/broad/Alignment.wdl' in files or
        'tasks/broad/BamProcessing.wdl' in files or
        'tasks/broad/BamToCram.wdl' in files or
        'tasks/broad/CopyFilesFromCloudToCloud.wdl' in files or
        'tasks/broad/GermlineVariantDiscovery.wdl' in files or
        'tasks/broad/Qc.wdl' in files or
        'tasks/broad/SplitLargeReadGroup.wdl' in files or
        'tasks/broad/UnmappedBamToAlignedBam.wdl' in files or
        'tasks/broad/Utilities.wdl' in files or
        'verification/VerifyGermlineSingleSample.wdl' in files or
        'verification/VerifyMetrics.wdl' in files or
        'verification/VerifyReprocessing.wdl' in files or
        'verification/VerifyTasks.wdl' in files or
        'pipelines/broad/dna_seq/germline/single_sample/exome' in files or
        'pipelines/broad/dna_seq/germline/single_sample/wgs' in files or
        'pipelines/broad/reprocessing/cram_to_unmapped_bams' in files or
        'pipelines/broad/reprocessing/exome' in files or
        'pipelines/broad/reprocessing/external' in files or
        'pipelines/broad/reprocessing/wgs' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 2
    reviewers:
      users:
        - ldgauthier # Laura Gauthier
        - kachulis # Chris Kachulis

  scientific_owners_joint_genotyping:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl' in files or
        'tasks/broad/JointGenotypingTasks.wdl' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.options.json' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/exome' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/reblocking' in files or
        'pipelines/broad/dna_seq/germline/joint_genotyping/wgs' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 1
      request_order: given
    reviewers:
      users:
        - ldgauthier # Laura Gauthier

  scientific_owners_somatic_single_sample:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl' in files or
        'structs/dna_seq/DNASeqStructs.wdl' in files or
        'tasks/broad/AggregatedBamQC.wdl' in files or
        'tasks/broad/Alignment.wdl' in files or
        'tasks/broad/BamProcessing.wdl' in files or
        'tasks/broad/BamToCram.wdl' in files or
        'tasks/broad/Qc.wdl' in files or
        'tasks/broad/SplitLargeReadGroup.wdl' in files or
        'tasks/broad/UnmappedBamToAlignedBam.wdl' in files or
        'tasks/broad/Utilities.wdl' in files or
        'beta-pipelines/broad/somatic/single_sample/targeted/README.md' in files or
        'beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.changelog.md' in files or
        'beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.options.json' in files or
        'beta-pipelines/broad/somatic/single_sample/targeted/TargetedSomaticSingleSample.wdl' in files or
        'beta-pipelines/broad/somatic/single_sample/targeted/test_inputs' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 1
      request_order: given
    reviewers:
      users:
        - fleharty # Mark Fleharty

  scientific_owners_imputation:
    conditions:
      - "'eng-only' not in labels"
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/arrays/imputation/Imputation.wdl' in files or
        'structs/imputation/ImputationStructs.wdl' in files or
        'tasks/broad/ImputationTasks.wdl' in files or
        'tasks/broad/Utilities.wdl' in files or
        'pipelines/broad/arrays/imputation/Imputation.changelog.md' in files or
        'pipelines/broad/arrays/imputation/Imputation.options.json' in files or
        'pipelines/broad/arrays/imputation/Imputation.wdl' in files or
        'pipelines/broad/arrays/imputation/example_inputs.json' in files
        
    reviews:
      required: 1
      author_value: 1
      request: 1
      request_order: given
    reviewers:
      users:
        - kachulis # Chris Kachulis


  # Clinical reviews:
  # - Approval is not required, this is just to send an email to Betty
  #   to make sure that she is aware of changes to the clinical pipelines
  clinical_owners:
    conditions:
      - "base.ref != 'master'"
      - "base.ref != 'staging'"
      - >
        'pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl' in files or
        'pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl' in files or
        'structs/dna_seq/DNASeqStructs.wdl' in files or
        'tasks/broad/AggregatedBamQC.wdl' in files or
        'tasks/broad/Alignment.wdl' in files or
        'tasks/broad/BamProcessing.wdl' in files or
        'tasks/broad/BamToCram.wdl' in files or
        'tasks/broad/GermlineVariantDiscovery.wdl' in files or
        'tasks/broad/Qc.wdl' in files or
        'tasks/broad/SplitLargeReadGroup.wdl' in files or
        'tasks/broad/UnmappedBamToAlignedBam.wdl' in files or
        'tasks/broad/Utilities.wdl' in files
        
    reviews:
      required: 0
      request: 1
    reviewers:
      users:
        - bwoolf2 # Betty Woolf