cloudgene.pgs.yaml

id: imputationserver2-pgs
name: Polygenic Score Calculation
description: "You can upload genotyped data and the application imputes your genotypes, performs ancestry estimation and finally calculates Polygenic Risk Scores.<br><br>No dataset at hand? No problem, download our example dataset: <a href=\"https://imputationserver.sph.umich.edu/resources/50-samples.zip\" class=\"btn btn-sm btn-secondary\" style=\"color:#ffffff !important\"><i class=\"fa fa-file\"></i> 50-samples.zip</a><br><br>"
version: 2.0.7
website: https://imputationserver.readthedocs.io
category: Application
submitButton: Start Calculation

workflow:
  steps:
    - name: Quality Control and Imputation
      type: nextflow
      script: main.nf
      # params without UI
      params:
        project: "${CLOUDGENE_JOB_NAME}"
        files: "${files}/*.vcf.gz"
        mode: "imputation"
        allele_frequency_population: "off"
        phasing:
          engine: "eagle"
        encryption:
          aes: false
        imputation:
          meta: false
          min_r2: ${r2Filter}          
        pgs:
          enabled: true
          category: "${pgs_category}"
        merge_results: false #no merge and encryption
        user:
          email: "${CLOUDGENE_USER_EMAIL}"
          name: "${CLOUDGENE_USER_NAME}"
        service:
          name: "${CLOUDGENE_SERVICE_NAME}"
          contact: "${CLOUDGENE_CONTACT_NAME}"
          email: "${CLOUDGENE_CONTACT_EMAIL}"
          url: "${CLOUDGENE_SERVICE_URL}"
      groups:
        - id: validation
          label: "Input Validation"
        - id: qc
          label: "Quality Control"          
        - id: imputation
          label: "Phasing and Imputation"
        - id: ancestry
          label: "Ancestry Estimation"  
        - id: pgs
          label: "Polygenic Scores"                           
      processes:
        - process: "INPUT_VALIDATION:INPUT_VALIDATION_VCF"
          view: status
          label: "Input Validation"
          group: "validation"
        - process: "QUALITY_CONTROL:QUALITY_CONTROL_VCF"
          view: status
          label: "Quality Control"
          group: "qc"
        - process: "QUALITY_CONTROL:QUALITY_CONTROL_REPORT"
          view: label
          label: "Quality Control Report"
          group: "qc"
        - process: "PHASING:EAGLE"
          view: progressbar
          label: "Phasing with Eagle"
          group: "imputation"
        - process: "PHASING:BEAGLE"
          view: progressbar
          label: "Phasing with Beagle"
          group: "imputation"
        - process: "IMPUTATION:MINIMAC4"
          view: progressbar
          label: "Imputation"
          group: "imputation"
        - process: "PGS_CALCULATION:FILTER_BY_CATEGORY"        
          view: status
          label: "Prepare Polygenic Scores"
          group: "pgs"
        - process: "PGS_CALCULATION:CALCULATE_CHUNKS"
          view: progressbar
          label: "Calculate Polygenic Scores"
          group: "pgs"
        - process: "ENCRYPTION:COMPRESSION_ENCRYPTION_VCF"
          view: label
          label: "Compression and Encryption"
          group: "pgs"
        - process: "PGS_CALCULATION:MERGE_CHUNKS_SCORES"
          view: label
          label: "Merge Polygenic Scores"
          group: "pgs"
        - process: "PGS_CALCULATION:MERGE_CHUNKS_INFOS"
          view: label
          label: "Analyze Polygenic Scores "
          group: "pgs"
        - process: "PGS_CALCULATION:CREATE_HTML_REPORT"
          view: label
          label: "Create Ploygenic Score Report"
          group: "pgs"
        - process: "ANCESTRY_ESTIMATION:PREPARE_TRACE"
          view: progressbar
          label: "Prepare Data"
          group: "ancestry"          
        - process: "ANCESTRY_ESTIMATION:EXECUTE_TRACE"
          view: progressbar
          label: "Prepare Data"
          group: "ancestry"
        - process: "ANCESTRY_ESTIMATION:ESTIMATE_ANCESTRY"
          view: label
          label: "Estimate Ancestry"
          group: "ancestry"
        - process: "ANCESTRY_ESTIMATION:VISUALIZE_ANCESTRY"
          view: label
          label: "Visualize Ancestry"
          group: "ancestry"                     
  inputs:
    - id: refpanel
      description: Reference Panel (<a href="https://imputationserver.sph.umich.edu/start.html#!pages/refpanels" target="_blank">Details</a>)
      type: app_list
      category: RefPanel

    - id: files
      description: Input Files (<a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41" target="_blank">VCF</a>)
      type: local_folder
      serialize: false

    - id: build
      description: Array Build
      type: list
      value: hg19
      values:
        hg19: GRCh37/hg19
        hg38: GRCh38/hg38
      details: Please note that the final SNP coordinates always match the reference build.

    - id: r2Filter
      description: rsq Filter
      type: list
      value: 0.3
      values:
        0: off
        0.3: 0.3
        0.8: 0.8
      serialize: false
      
    - id: myseparator0
      type: group

    - id: info2
      type: info
      description: <b>PGS Calculation</b><br><small class="text-muted">Please select a collection of polygenic scores to enable on the fly PGS calculation.</small>

    - id: pgscatalog
      description: Scores
      type: app_list
      required: true
      category: PGSPanel

    - id: pgs_category
      description: Trait Category
      type: list
      values:
        bind: pgscatalog
        property: categories
        category: PGSPanel
      serialize: false

    - id: ancestry
      description: Ancestry Estimation
      type: app_list
      required: false
      category: AncestryPanel
      emptySelection: Disabled

    - id: myseparator
      type: separator

    - id: password
      description: Password set by user.
      value:
      visible: false
      type: text
      
    - id: check1
      description: I will not attempt to re-identify or contact research participants.
      type: terms_checkbox

    - id: check2
      description: I will report any inadvertent data release, security breach or other data management incident of which I become aware.
      type: terms_checkbox

  outputs:
    - id: output
      description: Downloads
      type: local_folder
      download: true