WGS Germline (Multi callers)

WGSGermlineMultiCallers · A variant-calling WGS pipeline using GATK, VarDict and Strelka2 · 3 contributors · 1 version

This is a genomics pipeline to align sequencing data (Fastq pairs) into BAMs and call variants using:

This workflow is a reference pipeline using the Janis Python framework (pipelines assistant).

  • Takes raw sequence data in the FASTQ format;
  • Align to the reference genome using BWA MEM;
  • Marks duplicates using Picard;
  • Call the appropriate variant callers (GRIDSS / GATK / Strelka / VarDict);
  • Merges the variants from GATK / Strelka / VarDict.
  • Outputs the final variants in the VCF format.

Resources

This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:

This pipeline expects the assembly references to be as they appear in that storage (“.fai”, “.amb”, “.ann”, “.bwt”, “.pac”, “.sa”, “^.dict”). The known sites (snps_dbsnp, snps_1000gp, known_indels, mills_indels) should be gzipped and tabix indexed.

Quickstart

  1. Install Janis
  2. Ensure Janis is configured to work with Docker or Singularity.
  3. Ensure all reference files are available:

Note

More information about these inputs are available below.

Name Type Source Description
reference FastaWithIndexes
  • hg38: gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.fasta

The reference genome from which to align the reads. This requires a number indexes (can be generated with the ‘IndexFasta’ pipeline This pipeline has been tested using the HG38 reference set.

This pipeline expects the assembly references to be as they appear in the GCP example. For example:
  • (“.fai”, “.amb”, “.ann”, “.bwt”, “.pac”, “.sa”, “^.dict”).
snps_dbsnp Gzipped<VCF>
  • hg38: gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
 From the GATK resource bundle, passed to BaseRecalibrator as known_sites
snps_1000gp Gzipped<VCF>
  • hg38: gs://genomics-public-data/references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz
 From the GATK resource bundle, passed to BaseRecalibrator as known_sites. Accessible from the HG38 genomics-public-data google cloud bucket: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/
known_indels Gzipped<VCF>
  • hg38: gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz
 From the GATK resource bundle, passed to BaseRecalibrator as known_sites
mills_indels Gzipped<VCF>
  • hg38: gs://genomics-public-data/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
 From the GATK resource bundle, passed to BaseRecalibrator as known_sites
gridss_blacklist bed BED file containing regions to ignore. For more information, visit: https://github.com/PapenfussLab/gridss#blacklist
gatk_intervals Array<bed> None List of intervals over which to split the GATK variant calling
vardict_intervals Array<bed> None List of intervals over which to split the VarDict variant calling
strelka_intervals Gzipped<bed> None An interval for which to restrict the analysis to.
cutadapt_adapters File https://raw.githubusercontent.com/csf-ngs/fastqc/master/Contaminants/contaminant_list.txt
Specifies a containment list for cutadapt, which contains a list of sequences to determine valid
overrepresented sequences from the FastQC report to trim with Cuatadapt. The file must contain sets of named adapters in the form: name[tab]sequence. Lines prefixed with a hash will be ignored.
  1. Generate user and static input files for WGSGermlineMultiCallers:
# user inputs
janis inputs --user WGSGermlineMultiCallers > inputs.yaml

# static inputs
janis inputs --static WGSGermlineMultiCallers > static.yaml

inputs.yaml

fastqs:
- - sample1_R1.fastq.gz
  - sample1_R2.fastq.gz
- - sample1_R1-TOPUP.fastq.gz
  - sample1_R2-TOPUP.fastq.gz
sample_name: NA12878

static.yaml

cutadapt_adapters: contaminant_list.txt
gatk_intervals: BRCA1.bed
gridss_blacklist: gridss_blacklist.bed
known_indels: Homo_sapiens_assembly38.known_indels.vcf.gz
mills_indels: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
reference: Homo_sapiens_assembly38.fasta
snps_1000gp: 1000G_phase1.snps.high_confidence.hg38.vcf.gz
snps_dbsnp: Homo_sapiens_assembly38.dbsnp138.vcf.gz
strelka_intervals: BRCA1.bed.gz
vardict_intervals: BRCA1.bed
  1. Run WGSGermlineMultiCallers with:
janis run [...run options] \
    --inputs inputs.yaml \
    --inputs static.yaml \
    WGSGermlineMultiCallers

Outputs

name type documentation
out_fastqc_reports Array<Array<Zip>> A zip file of the FastQC quality report.
out_bam IndexedBam Aligned and indexed bam.
out_performance_summary csv A text file of performance summary of bam
out_gridss_assembly BAM Assembly returned by GRIDSS
out_variants_gridss VCF Variants from the GRIDSS variant caller
out_variants_gatk Gzipped<VCF> Merged variants from the GATK caller
out_variants_gatk_split Array<VCF> Unmerged variants from the GATK caller (by interval)
out_variants_strelka VCF Variants from the Strelka variant caller
out_variants_vardict Gzipped<VCF> Merged variants from the VarDict caller
out_variants_vardict_split Array<VCF> Unmerged variants from the VarDict caller (by interval)
out_variants VCF Combined variants from all 3 callers

Workflow

../_images/WGSGermlineMultiCallers_1_4_0.dot.png

Information

ID:WGSGermlineMultiCallers
Versions:1.4.0
Authors:Michael Franklin, Richard Lupat, Jiaan Yu
Citations:
Created:None
Updated:None

Embedded Tools

FastQC fastqc/v0.11.8
Parse FastQC Adaptors ParseFastqcAdaptors/v0.1.0
Align and sort reads BwaAligner/1.0.0
Merge and Mark Duplicates mergeAndMarkBams/4.1.3
Generate genome for BedtoolsCoverage GenerateGenomeFileForBedtoolsCoverage/v0.1.0
Performance summary workflow (whole genome) PerformanceSummaryGenome/v0.1.0
Gridss gridss/v2.6.2
GATK Base Recalibration on Bam GATKBaseRecalBQSRWorkflow/4.1.3
GATK4 Germline Variant Caller GATK4_GermlineVariantCaller/4.1.3.0
GATK4: Gather VCFs Gatk4GatherVcfs/4.1.3.0
BGZip bgzip/1.2.1
BCFTools: Sort bcftoolssort/v1.9
UncompressArchive UncompressArchive/v1.0.0
Strelka Germline Variant Caller strelkaGermlineVariantCaller/v0.1.1
GenerateVardictHeaderLines GenerateVardictHeaderLines/v0.1.0
Vardict Germline Variant Caller vardictGermlineVariantCaller/v0.1.1
Combine Variants combinevariants/0.0.8
Annotate Bam Stats to Germline Vcf Workflow AddBamStatsGermline/v0.1.0

Additional configuration (inputs)

name type documentation
sample_name String Sample name from which to generate the readGroupHeaderLine for BwaMem
fastqs Array<FastqGzPair> An array of FastqGz pairs. These are aligned separately and merged to create higher depth coverages from multiple sets of reads
reference FastaWithIndexes

The reference genome from which to align the reads. This requires a number indexes (can be generated with the ‘IndexFasta’ pipeline This pipeline has been tested using the HG38 reference set.

This pipeline expects the assembly references to be as they appear in the GCP example. For example:
  • (“.fai”, “.amb”, “.ann”, “.bwt”, “.pac”, “.sa”, “^.dict”).
snps_dbsnp Gzipped<VCF> From the GATK resource bundle, passed to BaseRecalibrator as known_sites
snps_1000gp Gzipped<VCF> From the GATK resource bundle, passed to BaseRecalibrator as known_sites. Accessible from the HG38 genomics-public-data google cloud bucket: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/
known_indels Gzipped<VCF> From the GATK resource bundle, passed to BaseRecalibrator as known_sites
mills_indels Gzipped<VCF> From the GATK resource bundle, passed to BaseRecalibrator as known_sites
gridss_blacklist bed BED file containing regions to ignore. For more information, visit: https://github.com/PapenfussLab/gridss#blacklist
gatk_intervals Array<bed> List of intervals over which to split the GATK variant calling
vardict_intervals Array<bed> List of intervals over which to split the VarDict variant calling
strelka_intervals Gzipped<bed> An interval for which to restrict the analysis to.
cutadapt_adapters File
Specifies a containment list for cutadapt, which contains a list of sequences to determine valid
overrepresented sequences from the FastQC report to trim with Cuatadapt. The file must contain sets of named adapters in the form: name[tab]sequence. Lines prefixed with a hash will be ignored.
align_and_sort_sortsam_tmpDir Optional<String> Undocumented option
vc_vardict_allele_freq_threshold Optional<Float>  
combine_variants_type Optional<String> germline | somatic
combine_variants_columns Optional<Array<String>> Columns to keep, seperated by space output vcf (unsorted)

Workflow Description Language

version development

import "tools/fastqc_v0_11_8.wdl" as F
import "tools/ParseFastqcAdaptors_v0_1_0.wdl" as P
import "tools/BwaAligner_1_0_0.wdl" as B
import "tools/mergeAndMarkBams_4_1_3.wdl" as M
import "tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.wdl" as G
import "tools/PerformanceSummaryGenome_v0_1_0.wdl" as P2
import "tools/gridss_v2_6_2.wdl" as G2
import "tools/GATKBaseRecalBQSRWorkflow_4_1_3.wdl" as G3
import "tools/GATK4_GermlineVariantCaller_4_1_3_0.wdl" as G4
import "tools/Gatk4GatherVcfs_4_1_3_0.wdl" as G5
import "tools/bgzip_1_2_1.wdl" as B2
import "tools/bcftoolssort_v1_9.wdl" as B3
import "tools/UncompressArchive_v1_0_0.wdl" as U
import "tools/strelkaGermlineVariantCaller_v0_1_1.wdl" as S
import "tools/GenerateVardictHeaderLines_v0_1_0.wdl" as G6
import "tools/vardictGermlineVariantCaller_v0_1_1.wdl" as V
import "tools/combinevariants_0_0_8.wdl" as C
import "tools/AddBamStatsGermline_v0_1_0.wdl" as A

workflow WGSGermlineMultiCallers {
  input {
    String sample_name
    Array[Array[File]] fastqs
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    File snps_dbsnp
    File snps_dbsnp_tbi
    File snps_1000gp
    File snps_1000gp_tbi
    File known_indels
    File known_indels_tbi
    File mills_indels
    File mills_indels_tbi
    File gridss_blacklist
    Array[File] gatk_intervals
    Array[File] vardict_intervals
    File strelka_intervals
    File strelka_intervals_tbi
    File cutadapt_adapters
    String? align_and_sort_sortsam_tmpDir = "./tmp"
    Float? vc_vardict_allele_freq_threshold = 0.05
    String? combine_variants_type = "germline"
    Array[String]? combine_variants_columns = ["AC", "AN", "AF", "AD", "DP", "GT"]
  }
  scatter (f in fastqs) {
     call F.fastqc as fastqc {
      input:
        reads=f
    }
  }
  scatter (f in fastqc.datafile) {
     call P.ParseFastqcAdaptors as getfastqc_adapters {
      input:
        fastqc_datafiles=f,
        cutadapt_adaptors_lookup=cutadapt_adapters
    }
  }
  scatter (Q in zip(fastqs, zip(getfastqc_adapters.adaptor_sequences, getfastqc_adapters.adaptor_sequences))) {
     call B.BwaAligner as align_and_sort {
      input:
        sample_name=sample_name,
        reference=reference,
        reference_fai=reference_fai,
        reference_amb=reference_amb,
        reference_ann=reference_ann,
        reference_bwt=reference_bwt,
        reference_pac=reference_pac,
        reference_sa=reference_sa,
        reference_dict=reference_dict,
        fastq=Q.left,
        cutadapt_adapter=Q.right.right,
        cutadapt_removeMiddle3Adapter=Q.right.right,
        sortsam_tmpDir=select_first([align_and_sort_sortsam_tmpDir, "./tmp"])
    }
  }
  call M.mergeAndMarkBams as merge_and_mark {
    input:
      bams=align_and_sort.out,
      bams_bai=align_and_sort.out_bai,
      sampleName=sample_name
  }
  call G.GenerateGenomeFileForBedtoolsCoverage as calculate_performancesummary_genomefile {
    input:
      reference=reference,
      reference_dict=reference_dict
  }
  call P2.PerformanceSummaryGenome as performance_summary {
    input:
      bam=merge_and_mark.out,
      bam_bai=merge_and_mark.out_bai,
      sample_name=sample_name,
      genome_file=calculate_performancesummary_genomefile.out
  }
  call G2.gridss as vc_gridss {
    input:
      bams=[merge_and_mark.out],
      bams_bai=[merge_and_mark.out_bai],
      reference=reference,
      reference_fai=reference_fai,
      reference_amb=reference_amb,
      reference_ann=reference_ann,
      reference_bwt=reference_bwt,
      reference_pac=reference_pac,
      reference_sa=reference_sa,
      reference_dict=reference_dict,
      blacklist=gridss_blacklist
  }
  scatter (g in gatk_intervals) {
     call G3.GATKBaseRecalBQSRWorkflow as bqsr {
      input:
        bam=merge_and_mark.out,
        bam_bai=merge_and_mark.out_bai,
        intervals=g,
        reference=reference,
        reference_fai=reference_fai,
        reference_amb=reference_amb,
        reference_ann=reference_ann,
        reference_bwt=reference_bwt,
        reference_pac=reference_pac,
        reference_sa=reference_sa,
        reference_dict=reference_dict,
        snps_dbsnp=snps_dbsnp,
        snps_dbsnp_tbi=snps_dbsnp_tbi,
        snps_1000gp=snps_1000gp,
        snps_1000gp_tbi=snps_1000gp_tbi,
        known_indels=known_indels,
        known_indels_tbi=known_indels_tbi,
        mills_indels=mills_indels,
        mills_indels_tbi=mills_indels_tbi
    }
  }
  scatter (Q in zip(gatk_intervals, transpose([bqsr.out, bqsr.out_bai]))) {
     call G4.GATK4_GermlineVariantCaller as vc_gatk {
      input:
        bam=Q.right[0],
        bam_bai=Q.right[1],
        intervals=Q.left,
        reference=reference,
        reference_fai=reference_fai,
        reference_amb=reference_amb,
        reference_ann=reference_ann,
        reference_bwt=reference_bwt,
        reference_pac=reference_pac,
        reference_sa=reference_sa,
        reference_dict=reference_dict,
        snps_dbsnp=snps_dbsnp,
        snps_dbsnp_tbi=snps_dbsnp_tbi
    }
  }
  call G5.Gatk4GatherVcfs as vc_gatk_merge {
    input:
      vcfs=vc_gatk.out
  }
  call B2.bgzip as vc_gatk_compress_for_sort {
    input:
      file=vc_gatk_merge.out
  }
  call B3.bcftoolssort as vc_gatk_sort_combined {
    input:
      vcf=vc_gatk_compress_for_sort.out
  }
  call U.UncompressArchive as vc_gatk_uncompress_for_combine {
    input:
      file=vc_gatk_sort_combined.out
  }
  call S.strelkaGermlineVariantCaller as vc_strelka {
    input:
      bam=merge_and_mark.out,
      bam_bai=merge_and_mark.out_bai,
      reference=reference,
      reference_fai=reference_fai,
      reference_amb=reference_amb,
      reference_ann=reference_ann,
      reference_bwt=reference_bwt,
      reference_pac=reference_pac,
      reference_sa=reference_sa,
      reference_dict=reference_dict,
      intervals=strelka_intervals,
      intervals_tbi=strelka_intervals_tbi
  }
  call G6.GenerateVardictHeaderLines as generate_vardict_headerlines {
    input:
      reference=reference,
      reference_dict=reference_dict
  }
  scatter (v in vardict_intervals) {
     call V.vardictGermlineVariantCaller as vc_vardict {
      input:
        bam=merge_and_mark.out,
        bam_bai=merge_and_mark.out_bai,
        intervals=v,
        sample_name=sample_name,
        allele_freq_threshold=select_first([vc_vardict_allele_freq_threshold, 0.05]),
        header_lines=generate_vardict_headerlines.out,
        reference=reference,
        reference_fai=reference_fai,
        reference_amb=reference_amb,
        reference_ann=reference_ann,
        reference_bwt=reference_bwt,
        reference_pac=reference_pac,
        reference_sa=reference_sa,
        reference_dict=reference_dict
    }
  }
  call G5.Gatk4GatherVcfs as vc_vardict_merge {
    input:
      vcfs=vc_vardict.out
  }
  call B2.bgzip as vc_vardict_compress_for_sort {
    input:
      file=vc_vardict_merge.out
  }
  call B3.bcftoolssort as vc_vardict_sort_combined {
    input:
      vcf=vc_vardict_compress_for_sort.out
  }
  call U.UncompressArchive as vc_vardict_uncompress_for_combine {
    input:
      file=vc_vardict_sort_combined.out
  }
  call C.combinevariants as combine_variants {
    input:
      vcfs=[vc_gatk_uncompress_for_combine.out, vc_strelka.out, vc_vardict_uncompress_for_combine.out],
      type=select_first([combine_variants_type, "germline"]),
      columns=select_first([combine_variants_columns, ["AC", "AN", "AF", "AD", "DP", "GT"]])
  }
  call B2.bgzip as combined_compress {
    input:
      file=combine_variants.out
  }
  call B3.bcftoolssort as combined_sort {
    input:
      vcf=combined_compress.out
  }
  call U.UncompressArchive as combined_uncompress {
    input:
      file=combined_sort.out
  }
  call A.AddBamStatsGermline as combined_addbamstats {
    input:
      bam=merge_and_mark.out,
      bam_bai=merge_and_mark.out_bai,
      vcf=combined_uncompress.out,
      reference=reference,
      reference_fai=reference_fai,
      reference_amb=reference_amb,
      reference_ann=reference_ann,
      reference_bwt=reference_bwt,
      reference_pac=reference_pac,
      reference_sa=reference_sa,
      reference_dict=reference_dict
  }
  output {
    Array[Array[File]] out_fastqc_reports = fastqc.out
    File out_bam = merge_and_mark.out
    File out_bam_bai = merge_and_mark.out_bai
    File out_performance_summary = performance_summary.performanceSummaryOut
    File out_gridss_assembly = vc_gridss.assembly
    File out_variants_gridss = vc_gridss.out
    File out_variants_gatk = vc_gatk_sort_combined.out
    Array[File] out_variants_gatk_split = vc_gatk.out
    File out_variants_strelka = vc_strelka.out
    File out_variants_vardict = vc_vardict_sort_combined.out
    Array[File] out_variants_vardict_split = vc_vardict.out
    File out_variants = combined_addbamstats.out
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: WGS Germline (Multi callers)
doc: |
  This is a genomics pipeline to align sequencing data (Fastq pairs) into BAMs and call variants using:

  This workflow is a reference pipeline using the Janis Python framework (pipelines assistant).

  - Takes raw sequence data in the FASTQ format;
  - Align to the reference genome using BWA MEM;
  - Marks duplicates using Picard;
  - Call the appropriate variant callers (GRIDSS / GATK / Strelka / VarDict);
  - Merges the variants from GATK / Strelka / VarDict.
  - Outputs the final variants in the VCF format.

  **Resources**

  This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:

  - https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/

  This pipeline expects the assembly references to be as they appear in that storage     (".fai", ".amb", ".ann", ".bwt", ".pac", ".sa", "^.dict").
  The known sites (snps_dbsnp, snps_1000gp, known_indels, mills_indels) should be gzipped and tabix indexed.

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement

inputs:
- id: sample_name
  doc: Sample name from which to generate the readGroupHeaderLine for BwaMem
  type: string
- id: fastqs
  doc: |-
    An array of FastqGz pairs. These are aligned separately and merged to create higher depth coverages from multiple sets of reads
  type:
    type: array
    items:
      type: array
      items: File
- id: reference
  doc: |2-
        The reference genome from which to align the reads. This requires a number indexes (can be generated     with the 'IndexFasta' pipeline This pipeline has been tested using the HG38 reference set.

        This pipeline expects the assembly references to be as they appear in the GCP example. For example:
            - HG38: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/

        - (".fai", ".amb", ".ann", ".bwt", ".pac", ".sa", "^.dict").
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
- id: snps_dbsnp
  doc: From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: snps_1000gp
  doc: |-
    From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``. Accessible from the HG38 genomics-public-data google cloud bucket: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: known_indels
  doc: From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: mills_indels
  doc: From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: gridss_blacklist
  doc: |-
    BED file containing regions to ignore. For more information, visit: https://github.com/PapenfussLab/gridss#blacklist
  type: File
- id: gatk_intervals
  doc: List of intervals over which to split the GATK variant calling
  type:
    type: array
    items: File
- id: vardict_intervals
  doc: List of intervals over which to split the VarDict variant calling
  type:
    type: array
    items: File
- id: strelka_intervals
  doc: An interval for which to restrict the analysis to.
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: cutadapt_adapters
  doc: |2-
                    Specifies a containment list for cutadapt, which contains a list of sequences to determine valid
                    overrepresented sequences from the FastQC report to trim with Cuatadapt. The file must contain sets
                    of named adapters in the form: ``name[tab]sequence``. Lines prefixed with a hash will be ignored.
  type: File
- id: align_and_sort_sortsam_tmpDir
  doc: Undocumented option
  type: string
  default: ./tmp
- id: vc_vardict_allele_freq_threshold
  type: float
  default: 0.05
- id: combine_variants_type
  doc: germline | somatic
  type: string
  default: germline
- id: combine_variants_columns
  doc: Columns to keep, seperated by space output vcf (unsorted)
  type:
    type: array
    items: string
  default:
  - AC
  - AN
  - AF
  - AD
  - DP
  - GT

outputs:
- id: out_fastqc_reports
  doc: A zip file of the FastQC quality report.
  type:
    type: array
    items:
      type: array
      items: File
  outputSource: fastqc/out
- id: out_bam
  doc: Aligned and indexed bam.
  type: File
  secondaryFiles:
  - pattern: .bai
  outputSource: merge_and_mark/out
- id: out_performance_summary
  doc: A text file of performance summary of bam
  type: File
  outputSource: performance_summary/performanceSummaryOut
- id: out_gridss_assembly
  doc: Assembly returned by GRIDSS
  type: File
  outputSource: vc_gridss/assembly
- id: out_variants_gridss
  doc: Variants from the GRIDSS variant caller
  type: File
  outputSource: vc_gridss/out
- id: out_variants_gatk
  doc: Merged variants from the GATK caller
  type: File
  outputSource: vc_gatk_sort_combined/out
- id: out_variants_gatk_split
  doc: Unmerged variants from the GATK caller (by interval)
  type:
    type: array
    items: File
  outputSource: vc_gatk/out
- id: out_variants_strelka
  doc: Variants from the Strelka variant caller
  type: File
  outputSource: vc_strelka/out
- id: out_variants_vardict
  doc: Merged variants from the VarDict caller
  type: File
  outputSource: vc_vardict_sort_combined/out
- id: out_variants_vardict_split
  doc: Unmerged variants from the VarDict caller (by interval)
  type:
    type: array
    items: File
  outputSource: vc_vardict/out
- id: out_variants
  doc: Combined variants from all 3 callers
  type: File
  outputSource: combined_addbamstats/out

steps:
- id: fastqc
  label: FastQC
  in:
  - id: reads
    source: fastqs
  scatter:
  - reads
  run: tools/fastqc_v0_11_8.cwl
  out:
  - id: out
  - id: datafile
- id: getfastqc_adapters
  label: Parse FastQC Adaptors
  in:
  - id: fastqc_datafiles
    source: fastqc/datafile
  - id: cutadapt_adaptors_lookup
    source: cutadapt_adapters
  scatter:
  - fastqc_datafiles
  run: tools/ParseFastqcAdaptors_v0_1_0.cwl
  out:
  - id: adaptor_sequences
- id: align_and_sort
  label: Align and sort reads
  in:
  - id: sample_name
    source: sample_name
  - id: reference
    source: reference
  - id: fastq
    source: fastqs
  - id: cutadapt_adapter
    source: getfastqc_adapters/adaptor_sequences
  - id: cutadapt_removeMiddle3Adapter
    source: getfastqc_adapters/adaptor_sequences
  - id: sortsam_tmpDir
    source: align_and_sort_sortsam_tmpDir
  scatter:
  - fastq
  - cutadapt_adapter
  - cutadapt_removeMiddle3Adapter
  scatterMethod: dotproduct
  run: tools/BwaAligner_1_0_0.cwl
  out:
  - id: out
- id: merge_and_mark
  label: Merge and Mark Duplicates
  in:
  - id: bams
    source: align_and_sort/out
  - id: sampleName
    source: sample_name
  run: tools/mergeAndMarkBams_4_1_3.cwl
  out:
  - id: out
- id: calculate_performancesummary_genomefile
  label: Generate genome for BedtoolsCoverage
  in:
  - id: reference
    source: reference
  run: tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.cwl
  out:
  - id: out
- id: performance_summary
  label: Performance summary workflow (whole genome)
  in:
  - id: bam
    source: merge_and_mark/out
  - id: sample_name
    source: sample_name
  - id: genome_file
    source: calculate_performancesummary_genomefile/out
  run: tools/PerformanceSummaryGenome_v0_1_0.cwl
  out:
  - id: performanceSummaryOut
- id: vc_gridss
  label: Gridss
  in:
  - id: bams
    source:
    - merge_and_mark/out
    linkMerge: merge_nested
  - id: reference
    source: reference
  - id: blacklist
    source: gridss_blacklist
  run: tools/gridss_v2_6_2.cwl
  out:
  - id: out
  - id: assembly
- id: bqsr
  label: GATK Base Recalibration on Bam
  in:
  - id: bam
    source: merge_and_mark/out
  - id: intervals
    source: gatk_intervals
  - id: reference
    source: reference
  - id: snps_dbsnp
    source: snps_dbsnp
  - id: snps_1000gp
    source: snps_1000gp
  - id: known_indels
    source: known_indels
  - id: mills_indels
    source: mills_indels
  scatter:
  - intervals
  run: tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl
  out:
  - id: out
- id: vc_gatk
  label: GATK4 Germline Variant Caller
  in:
  - id: bam
    source: bqsr/out
  - id: intervals
    source: gatk_intervals
  - id: reference
    source: reference
  - id: snps_dbsnp
    source: snps_dbsnp
  scatter:
  - intervals
  - bam
  scatterMethod: dotproduct
  run: tools/GATK4_GermlineVariantCaller_4_1_3_0.cwl
  out:
  - id: variants
  - id: out_bam
  - id: out
- id: vc_gatk_merge
  label: 'GATK4: Gather VCFs'
  in:
  - id: vcfs
    source: vc_gatk/out
  run: tools/Gatk4GatherVcfs_4_1_3_0.cwl
  out:
  - id: out
- id: vc_gatk_compress_for_sort
  label: BGZip
  in:
  - id: file
    source: vc_gatk_merge/out
  run: tools/bgzip_1_2_1.cwl
  out:
  - id: out
- id: vc_gatk_sort_combined
  label: 'BCFTools: Sort'
  in:
  - id: vcf
    source: vc_gatk_compress_for_sort/out
  run: tools/bcftoolssort_v1_9.cwl
  out:
  - id: out
- id: vc_gatk_uncompress_for_combine
  label: UncompressArchive
  in:
  - id: file
    source: vc_gatk_sort_combined/out
  run: tools/UncompressArchive_v1_0_0.cwl
  out:
  - id: out
- id: vc_strelka
  label: Strelka Germline Variant Caller
  in:
  - id: bam
    source: merge_and_mark/out
  - id: reference
    source: reference
  - id: intervals
    source: strelka_intervals
  run: tools/strelkaGermlineVariantCaller_v0_1_1.cwl
  out:
  - id: sv
  - id: variants
  - id: out
- id: generate_vardict_headerlines
  label: GenerateVardictHeaderLines
  in:
  - id: reference
    source: reference
  run: tools/GenerateVardictHeaderLines_v0_1_0.cwl
  out:
  - id: out
- id: vc_vardict
  label: Vardict Germline Variant Caller
  in:
  - id: bam
    source: merge_and_mark/out
  - id: intervals
    source: vardict_intervals
  - id: sample_name
    source: sample_name
  - id: allele_freq_threshold
    source: vc_vardict_allele_freq_threshold
  - id: header_lines
    source: generate_vardict_headerlines/out
  - id: reference
    source: reference
  scatter:
  - intervals
  run: tools/vardictGermlineVariantCaller_v0_1_1.cwl
  out:
  - id: variants
  - id: out
- id: vc_vardict_merge
  label: 'GATK4: Gather VCFs'
  in:
  - id: vcfs
    source: vc_vardict/out
  run: tools/Gatk4GatherVcfs_4_1_3_0.cwl
  out:
  - id: out
- id: vc_vardict_compress_for_sort
  label: BGZip
  in:
  - id: file
    source: vc_vardict_merge/out
  run: tools/bgzip_1_2_1.cwl
  out:
  - id: out
- id: vc_vardict_sort_combined
  label: 'BCFTools: Sort'
  in:
  - id: vcf
    source: vc_vardict_compress_for_sort/out
  run: tools/bcftoolssort_v1_9.cwl
  out:
  - id: out
- id: vc_vardict_uncompress_for_combine
  label: UncompressArchive
  in:
  - id: file
    source: vc_vardict_sort_combined/out
  run: tools/UncompressArchive_v1_0_0.cwl
  out:
  - id: out
- id: combine_variants
  label: Combine Variants
  in:
  - id: vcfs
    source:
    - vc_gatk_uncompress_for_combine/out
    - vc_strelka/out
    - vc_vardict_uncompress_for_combine/out
  - id: type
    source: combine_variants_type
  - id: columns
    source: combine_variants_columns
  run: tools/combinevariants_0_0_8.cwl
  out:
  - id: out
- id: combined_compress
  label: BGZip
  in:
  - id: file
    source: combine_variants/out
  run: tools/bgzip_1_2_1.cwl
  out:
  - id: out
- id: combined_sort
  label: 'BCFTools: Sort'
  in:
  - id: vcf
    source: combined_compress/out
  run: tools/bcftoolssort_v1_9.cwl
  out:
  - id: out
- id: combined_uncompress
  label: UncompressArchive
  in:
  - id: file
    source: combined_sort/out
  run: tools/UncompressArchive_v1_0_0.cwl
  out:
  - id: out
- id: combined_addbamstats
  label: Annotate Bam Stats to Germline Vcf Workflow
  in:
  - id: bam
    source: merge_and_mark/out
  - id: vcf
    source: combined_uncompress/out
  - id: reference
    source: reference
  run: tools/AddBamStatsGermline_v0_1_0.cwl
  out:
  - id: out
id: WGSGermlineMultiCallers