ExomeGermlineSingleSample.wdl

version 1.0

## Copyright Broad Institute, 2018
##
## This WDL pipeline implements data pre-processing and initial variant calling (GVCF
## generation) according to the GATK Best Practices (June 2016) for germline SNP and
## Indel discovery in human exome sequencing data.
##
## Requirements/expectations :
## - Human exome sequencing data in unmapped BAM (uBAM) format
## - One or more read groups, one per uBAM file, all belonging to a single sample (SM)
## - Input uBAM files must additionally comply with the following requirements:
## - - filenames all have the same suffix (we use ".unmapped.bam")
## - - files must pass validation by ValidateSamFile
## - - reads are provided in query-sorted order
## - - all reads must have an RG tag
## - GVCF output names must end in ".g.vcf.gz"
## - Reference genome must be Hg38 with ALT contigs
##
## Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
## For program versions, see docker containers.
##
## LICENSING :
## This script is released under the WDL source code license (BSD-3) (see LICENSE in
## https://github.com/broadinstitute/wdl). Note however that the programs it calls may
## be subject to different licenses. Users are responsible for checking that they are
## authorized to run all programs before running this script. Please see the docker
## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed
## licensing information pertaining to the included programs.

import "https://raw.githubusercontent.com/talkowski-lab/gatk4-exome-analysis-pipeline/master/tasks/GermlineVariantDiscovery.wdl" as Calling
import "https://raw.githubusercontent.com/talkowski-lab/gatk4-exome-analysis-pipeline/master/tasks/Qc.wdl" as QC
import "https://raw.githubusercontent.com/talkowski-lab/gatk4-exome-analysis-pipeline/master/tasks/Utilities.wdl" as Utils
import "https://raw.githubusercontent.com/talkowski-lab/gatk4-exome-analysis-pipeline/master/tasks/VariantCalling.wdl" as ToGvcf
import "https://raw.githubusercontent.com/talkowski-lab/gatk4-exome-analysis-pipeline/master/structs/GermlineStructs.wdl"

# WORKFLOW DEFINITION
workflow ExomeGermlineSingleSample {

  input {
    SampleAndUnmappedBams sample_and_unmapped_bams
    PapiSettings papi_settings
    GermlineSingleSampleReferences references

  }


  call ToGvcf.VariantCalling as BamToGvcf {
    input:
      calling_interval_list = references.calling_interval_list,
      evaluation_interval_list = references.evaluation_interval_list,
      haplotype_scatter_count = references.haplotype_scatter_count,
      break_bands_at_multiples_of = references.break_bands_at_multiples_of,
      input_bam = sample_and_unmapped_bams.input_cram,
      input_crai = sample_and_unmapped_bams.input_crai,
      ref_fasta = references.reference_fasta.ref_fasta,
      ref_fasta_index = references.reference_fasta.ref_fasta_index,
      ref_dict = references.reference_fasta.ref_dict,
      dbsnp_vcf = references.dbsnp_vcf,
      dbsnp_vcf_index = references.dbsnp_vcf_index,
      base_file_name = sample_and_unmapped_bams.base_file_name,
      final_vcf_base_name = sample_and_unmapped_bams.final_gvcf_base_name,
      agg_preemptible_tries = papi_settings.agg_preemptible_tries
  }


  # Outputs that will be retained when execution is complete
  output {
    File gvcf_summary_metrics = BamToGvcf.vcf_summary_metrics
    File gvcf_detail_metrics = BamToGvcf.vcf_detail_metrics
    File output_vcf = BamToGvcf.output_vcf
    File output_vcf_index = BamToGvcf.output_vcf_index
  }
}