diff --git a/tools/gatk_gathervcfscloud.cwl b/tools/gatk_gathervcfscloud.cwl
deleted file mode 100644
index b23ef16..0000000
--- a/tools/gatk_gathervcfscloud.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-id: gatk_gathervcfscloud
-requirements:
-  - class: DockerRequirement
-    dockerPull: 'kfdrc/gatk:4.0.5.2'
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: ResourceRequirement
-    ramMin: 7000
-    coresMin: 2
-hints:
-  - class: 'sbg:AWSInstanceType'
-    value: r4.2xlarge;ebs-gp2;500
-baseCommand: []
-arguments:
-  - position: 0
-    shellQuote: false
-    valueFrom: >-
-      /gatk --java-options "-Xmx6g -Xms6g"
-      GatherVcfsCloud
-      --ignore-safety-checks
-      --gather-type BLOCK
-      --output $(inputs.output_vcf_basename + ".vcf.gz")
-  - position: 2
-    shellQuote: false
-    valueFrom: >-
-      && /gatk IndexFeatureFile -F $(inputs.output_vcf_basename + ".vcf.gz")
-inputs:
-  input_vcfs:
-    type:
-      type: array
-      items: File
-      inputBinding:
-        prefix: -I
-    inputBinding:
-      position: 1
-  output_vcf_basename: string
-outputs:
-  output:
-    type: File
-    outputBinding:
-      glob: $(inputs.output_vcf_basename + ".vcf.gz")
-    secondaryFiles: [.tbi]
diff --git a/tools/gatk_genotypegvcfs.cwl b/tools/gatk_genotypegvcfs.cwl
deleted file mode 100644
index 7b57621..0000000
--- a/tools/gatk_genotypegvcfs.cwl
+++ /dev/null
@@ -1,43 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-id: gatk_genotypegvcfs
-requirements:
-  - class: DockerRequirement
-    dockerPull: 'broadinstitute/gatk:4.beta.5'
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: ResourceRequirement
-    ramMin: 7000
-    coresMin: 2
-baseCommand: []
-arguments:
-  - position: 0
-    shellQuote: false
-    valueFrom: >-
-      tar -xf $(inputs.workspace_tar.path)
-
-      /gatk/gatk-launch --javaOptions "-Xmx5g -Xms5g"
-      GenotypeGVCFs
-      -R $(inputs.ref_fasta.path)
-      -O output.vcf.gz
-      -D $(inputs.dbsnp_vcf.path)
-      -G StandardAnnotation
-      --onlyOutputCallsStartingInIntervals
-      -newQual
-      -V gendb://$(inputs.workspace_tar.nameroot)
-      -L $(inputs.interval.path)
-inputs:
-  workspace_tar: File
-  ref_fasta:
-    type: File
-    secondaryFiles: [^.dict, .fai]
-  dbsnp_vcf:
-    type: File
-    secondaryFiles: [.idx]
-  interval: File
-outputs:
-  output:
-    type: File
-    outputBinding:
-      glob: output.vcf.gz
-    secondaryFiles: [.tbi]
diff --git a/tools/gatk_hardfiltermakesitesonlyvcf.cwl b/tools/gatk_hardfiltermakesitesonlyvcf.cwl
deleted file mode 100644
index cc9fe52..0000000
--- a/tools/gatk_hardfiltermakesitesonlyvcf.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-id: gatk_hardfiltermakesitesonlyvcf
-requirements:
-  - class: DockerRequirement
-    dockerPull: 'kfdrc/gatk4-picard:4.beta.1-2.8.3'
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: ResourceRequirement
-    ramMin: 3500
-    coresMin: 1
-baseCommand: []
-arguments:
-  - position: 0
-    shellQuote: false
-    valueFrom: >-
-      /gatk-launch --javaOptions "-Xmx3g -Xms3g"
-      VariantFiltration
-      --filterExpression "ExcessHet > 54.69"
-      --filterName ExcessHet
-      -O variant_filtered.vcf.gz
-      -V $(inputs.vcf.path)
-
-      java -Xmx3g -Xms3g -jar /picard.jar
-      MakeSitesOnlyVcf
-      INPUT=variant_filtered.vcf.gz
-      OUTPUT=sites_only.variant_filtered.vcf.gz
-inputs:
-  vcf:
-    type: File
-    secondaryFiles: [.tbi]
-outputs:
-  variant_filtered_vcf:
-    type: File
-    outputBinding:
-      glob: variant_filtered.vcf.gz
-    secondaryFiles: [.tbi]
-  sites_only_vcf:
-    type: File
-    outputBinding:
-      glob: sites_only.variant_filtered.vcf.gz
-    secondaryFiles: [.tbi]
diff --git a/tools/kf_peddy_tool.cwl b/tools/kf_peddy_tool.cwl
deleted file mode 100644
index 7b66625..0000000
--- a/tools/kf_peddy_tool.cwl
+++ /dev/null
@@ -1,46 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-id: kfdrc-peddy-tool
-requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: ResourceRequirement
-    ramMin: 1000
-  - class: DockerRequirement
-    dockerPull: 'kfdrc/peddy:latest'
-baseCommand: [python]
-arguments:
-  - position: 1
-    shellQuote: false
-    valueFrom: >-
-      -m peddy
-      -p 4
-      --sites hg38
-      --prefix $(inputs.output_basename)
-      --plot
-      $(inputs.vqsr_vcf.path)
-      $(inputs.ped.path)
-
-inputs:
-  vqsr_vcf: {type: File, secondaryFiles: [.tbi]}
-  ped: File
-  output_basename: string
-outputs:
-  output_html:
-    type:
-      type: array
-      items: File
-    outputBinding:
-      glob: '*.html'
-  output_csv:
-    type:
-      type: array
-      items: File
-    outputBinding:
-      glob: '*_check.csv'
-  output_peddy:
-    type:
-      type: array
-      items: File
-    outputBinding:
-      glob: '*.peddy.ped'
diff --git a/tools/kf_sv2-sv-tool.cwl b/tools/kf_sv2-sv-tool.cwl
deleted file mode 100644
index 1f52670..0000000
--- a/tools/kf_sv2-sv-tool.cwl
+++ /dev/null
@@ -1,88 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-id: kfdrc-sv2-sv-tool
-requirements:
-  - class: InlineJavascriptRequirement
-  - class: ShellCommandRequirement
-  - class: ResourceRequirement
-    ramMin: 3000
-  - class: DockerRequirement
-    dockerPull: 'migbro/sv2:latest'
-  - class: MultipleInputFeatureRequirement
-baseCommand: ["/bin/bash", "-c"]
-arguments:
-  - position: 0
-    shellQuote: false
-    valueFrom: >-
-      set -eo pipefail
-
-      tar -xzf $(inputs.sv2_ref.path)
-      && /seq_cache_populate.pl
-      -root $PWD/ref_cache
-      $(inputs.reference.path)
-      && export REF_CACHE=$PWD/ref_cache/%2s/%2s/%s
-      && cp /usr/local/lib/python2.7/dist-packages/sv2/config/sv2.ini ./
-      && sed -i "s,sv2_resource = None,sv2_resource = $PWD," ./sv2.ini
-      && sed -i "s,hg38 = None,hg38 = $(inputs.reference.path)," ./sv2.ini
-      && cp /usr/local/lib/python2.7/dist-packages/sv2/resources/training_sets/*.pkl .
-      && sv2 -snv $(inputs.snv_vcf.path) -p $(inputs.ped.path) -g hg38 -ini ./sv2.ini -i
-  - position: 1
-    shellQuote: false
-    valueFrom: |
-      ${
-        var bams = inputs.input_cram[0].path
-        for (var i = 1; i < inputs.input_cram.length; i++){
-          bams += " "+inputs.input_cram[i].path
-        }
-        return bams
-      }
-  - position: 2
-    shellQuote: false
-    valueFrom: >-
-      -v
-  - position: 3
-    shellQuote: false
-    valueFrom: |
-      ${
-        var vcfs = inputs.sv_vcf[0].path
-        for (var i = 1; i < inputs.sv_vcf.length; i++){
-          vcfs += " "+inputs.sv_vcf[i].path
-        }
-        return vcfs
-      }
-  - position: 4
-    shellQuote: false
-    valueFrom: >-
-      && cat sv2_genotypes/sv2_genotypes.vcf
-      | bgzip -c > $(inputs.output_basename)_sv2_genotypes.vcf.gz
-      && tabix $(inputs.output_basename)_sv2_genotypes.vcf.gz
-      && mv sv2_genotypes/sv2_genotypes.txt $(inputs.output_basename)_sv2_genotypes.txt
-inputs:
-  reference: { type: File, secondaryFiles: [.fai] }
-  input_cram:
-    type:
-      type: array
-      items: File
-    secondaryFiles:
-      - .crai
-  sv_vcf:
-    type:
-      type: array
-      items: File
-    secondaryFiles:
-      - .tbi
-  snv_vcf: { type: File, secondaryFiles: [.tbi] }
-  ped: File
-  output_basename: string
-  sv2_ref: File
-
-outputs:
-  out_vcf:
-    type: File
-    outputBinding:
-      glob: '*.vcf.gz'
-    secondaryFiles: [.tbi]
-  out_txt:
-    type: File
-    outputBinding:
-      glob: '*.txt'
diff --git a/workflow/kf_jointgenotyping_workflow_optimized_and_refinement.cwl b/workflow/kf_jointgenotyping_workflow_optimized_and_refinement.cwl
deleted file mode 100644
index fb6c867..0000000
--- a/workflow/kf_jointgenotyping_workflow_optimized_and_refinement.cwl
+++ /dev/null
@@ -1,173 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: kf_jointgenotyping_workflow_optimized_and_refinement
-requirements:
-  - class: ScatterFeatureRequirement
-
-inputs:
-  input_vcfs: File[]
-  unpadded_intervals_file: File
-  dbsnp_vcf: File
-  output_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
-  ped: File
-  cache: File
-  snp_sites: File
-
-outputs:
-  collectvariantcallingmetrics:
-    type: File[]
-    outputSource: picard_collectvariantcallingmetrics/output
-  cgp_vep_annotated_vcf:
-    type: File
-    outputSource: vep_annotate/output_vcf
-  vcf_summary_stats:
-    type: File
-    outputSource: vep_annotate/output_txt
-  vep_warn:
-    type: File
-    outputSource: vep_annotate/warn_txt
-  output_html:
-    type: File[]
-    outputSource: peddy/output_html
-  output_csv:
-    type: File[]
-    outputSource: peddy/output_csv
-  output_peddy:
-    type: File[]
-    outputSource: peddy/output_peddy
-
-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_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_basename
-      dbsnp_vcf: dbsnp_vcf
-      wgs_evaluation_interval_list: wgs_evaluation_interval_list
-    out: [output]
-  gatk_calculategenotypeposteriors:
-    in:
-      ped: ped
-      reference: ref_fasta
-      snp_sites: snp_sites
-      vqsr_vcf: gatk_finalgathervcf/output
-      output_basename: output_basename
-    out: [output]
-    run: ../tools/gatk_calculategenotypeposteriors.cwl
-
-  gatk_variantfiltration:
-    in:
-      cgp_vcf: gatk_calculategenotypeposteriors/output
-      reference: ref_fasta
-      output_basename: output_basename
-    out: [output]
-    run: ../tools/gatk_variantfiltration.cwl
-  gatk_variantannotator:
-    in:
-      cgp_filtered_vcf: gatk_variantfiltration/output
-      ped: ped
-      reference: ref_fasta
-      output_basename: output_basename
-    out: [output]
-    run: ../tools/gatk_variantannotator.cwl
-  vep_annotate:
-    in:
-      input_vcf: gatk_variantannotator/output
-      reference: ref_fasta
-      output_basename: output_basename
-      cache: cache
-    out: [output]
-    run: ../tools/variant_effect_predictor.cwl
-  peddy:
-    in:
-      vqsr_vcf: gatk_finalgathervcf/output
-      ped: ped
-      output_basename: output_basename
-    out: [output]
-    run: ../tools/kf_peddy_tool.cwl
-
-$namespaces:
-  sbg: https://sevenbridges.com
-hints:
-  - class: 'sbg:maxNumberOfParallelInstances'
-    value: 2