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cwlVersion: v1.0
class: Workflow
id: kf_jointgenotyping_workflow_optimized
requirements:
- class: ScatterFeatureRequirement
inputs:
input_vcfs: File[]
unpadded_intervals_file: File
dbsnp_vcf: File
output_vcf_basename: string
ref_fasta: File
hapmap_resource_vcf: File
omni_resource_vcf: File
one_thousand_genomes_resource_vcf: File
axiomPoly_resource_vcf: File
mills_resource_vcf: File
reference_dict: File
wgs_evaluation_interval_list: File
outputs:
finalgathervcf:
type: File
outputSource: gatk_finalgathervcf/output
collectvariantcallingmetrics:
type: File[]
outputSource: picard_collectvariantcallingmetrics/output
steps:
dynamicallycombineintervals:
run: ../tools/script_dynamicallycombineintervals.cwl
in:
input_vcfs: input_vcfs
interval: unpadded_intervals_file
out: [out_intervals]
gatk_import_genotype_filtergvcf_merge:
run: ../tools/gatk_import_genotype_filtergvcf_merge.cwl
in:
input_vcfs: input_vcfs
interval: dynamicallycombineintervals/out_intervals
dbsnp_vcf: dbsnp_vcf
ref_fasta: ref_fasta
scatter: [interval]
out:
[variant_filtered_vcf, sites_only_vcf]
gatk_gathervcfs:
run: ../tools/gatk_gathervcfs.cwl
in:
input_vcfs: gatk_import_genotype_filtergvcf_merge/sites_only_vcf
out: [output]
gatk_snpsvariantrecalibratorcreatemodel:
run: ../tools/gatk_snpsvariantrecalibratorcreatemodel.cwl
in:
dbsnp_resource_vcf: dbsnp_vcf
hapmap_resource_vcf: hapmap_resource_vcf
omni_resource_vcf: omni_resource_vcf
one_thousand_genomes_resource_vcf: one_thousand_genomes_resource_vcf
sites_only_variant_filtered_vcf: gatk_gathervcfs/output
out: [model_report]
gatk_indelsvariantrecalibrator:
run: ../tools/gatk_indelsvariantrecalibrator.cwl
in:
axiomPoly_resource_vcf: axiomPoly_resource_vcf
dbsnp_resource_vcf: dbsnp_vcf
mills_resource_vcf: mills_resource_vcf
sites_only_variant_filtered_vcf: gatk_gathervcfs/output
out: [recalibration, tranches]
gatk_snpsvariantrecalibratorscattered:
run: ../tools/gatk_snpsvariantrecalibratorscattered.cwl
in:
sites_only_variant_filtered_vcf: gatk_import_genotype_filtergvcf_merge/sites_only_vcf
model_report: gatk_snpsvariantrecalibratorcreatemodel/model_report
hapmap_resource_vcf: hapmap_resource_vcf
omni_resource_vcf: omni_resource_vcf
one_thousand_genomes_resource_vcf: one_thousand_genomes_resource_vcf
dbsnp_resource_vcf: dbsnp_vcf
scatter: [sites_only_variant_filtered_vcf]
out: [recalibration, tranches]
gatk_gathertranches:
run: ../tools/gatk_gathertranches.cwl
in:
tranches: gatk_snpsvariantrecalibratorscattered/tranches
out: [output]
gatk_applyrecalibration:
run: ../tools/gatk_applyrecalibration.cwl
in:
indels_recalibration: gatk_indelsvariantrecalibrator/recalibration
indels_tranches: gatk_indelsvariantrecalibrator/tranches
input_vcf: gatk_import_genotype_filtergvcf_merge/variant_filtered_vcf
snps_recalibration: gatk_snpsvariantrecalibratorscattered/recalibration
snps_tranches: gatk_gathertranches/output
scatter: [input_vcf, snps_recalibration]
scatterMethod: dotproduct
out: [recalibrated_vcf]
gatk_finalgathervcf:
run: ../tools/gatk_gathervcfscloud.cwl
in:
input_vcfs: gatk_applyrecalibration/recalibrated_vcf
output_vcf_basename: output_vcf_basename
out: [output]
picard_collectvariantcallingmetrics:
run: ../tools/picard_collectvariantcallingmetrics.cwl
in:
input_vcf: gatk_finalgathervcf/output
reference_dict: reference_dict
final_gvcf_base_name: output_vcf_basename
dbsnp_vcf: dbsnp_vcf
wgs_evaluation_interval_list: wgs_evaluation_interval_list
out: [output]
$namespaces:
sbg: https://sevenbridges.com
hints:
- class: 'sbg:AWSInstanceType'
value: r4.2xlarge;ebs-gp2;500
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