cloudgene.yaml

id: mtdna-server-2
name: mtDNA-Server 2 - Mitochondrial Variant Calling 
description: "A free web service to analyze your mtDNA NGS data. The service accepts data in BAM format aligned against the rCRS reference and returns homoplasmic and heteroplasmic variants in return. <br>Feel free to <a href=\"https://github.com/genepi/mtdna-server-2/?tab=readme-ov-file#contact\"><u>contact us</u></a> if you have issues running the pipeline.<br><br>No dataset at hand? No problem, download and extract our example dataset: <a href=\"https://mitoverse.i-med.ac.at/downloads/6-samples.zip\" class=\"btn btn-sm btn-secondary\" style=\"color:#ffffff !important\"><i class=\"fa fa-file\"></i> 6-samples.zip</a><br><br>"

version: v2.1.16
website: https://mitoverse.readthedocs.io/
category:

workflow:
  steps:
    - name: mtDNA-Server 2 - Mitochondrial Variant Calling
      type: nextflow
      script: main.nf
      # params without UI
      params:
        project: "${CLOUDGENE_JOB_NAME}"
        user:
          email: "${CLOUDGENE_USER_EMAIL}"
          name: "${CLOUDGENE_USER_NAME}"
        service:
          name: "${CLOUDGENE_SERVICE_NAME}"
          email: "${CLOUDGENE_CONTACT_EMAIL}"
          url: "${CLOUDGENE_SERVICE_URL}"
      processes:
        - process: "MTDNA_SERVER_2:CALCULATE_STATISTICS"
          label: "Calculate Sample Statistics"
          view: progressbar
        - process: "MTDNA_SERVER_2:INDEX"
          label: "Index Reference"
          view: progressbar     
        - process: "MTDNA_SERVER_2:SUBSAMPLING"
          label: "Subsampling"
          view: progressbar               
        - process: "MTDNA_SERVER_2:INPUT_VALIDATION"
          label: "Input Validation"
          view: progressbar
        - process: "MTDNA_SERVER_2:QUALITY_CONTROL"
          label: "Quality Control Report"
          view: progressbar          
        - process: "MTDNA_SERVER_2:MUTSERVE"
          label: "Variant Calling (mutserve)"
          view: progressbar
        - process: "MTDNA_SERVER_2:MUTECT2"
          label: "Variant Calling (Mutect2)"
          view: progressbar  
        - process: "MTDNA_SERVER_2:FILTER_VARIANTS"
          label: "Filtering"       
          view: progressbar  
        - process: "MTDNA_SERVER_2:MERGING_VARIANTS"
          label: "Merging"
          view: progressbar            
        - process: "MTDNA_SERVER_2:ANNOTATE"
          label: "Annotation"
          view: progressbar
        - process: "MTDNA_SERVER_2:COVERAGE_ESTIMATION"
          label: "Estimating required VAF Coverage"
          view: progressbar          
        - process: "MTDNA_SERVER_2:HAPLOGROUPS_CONTAMINATION"
          label: "Haplogroups & Contamination Detection"
          view: progressbar
        - process: "MTDNA_SERVER_2:VCF_MERGE"
          label: "VCF Merge"
          view: progressbar
        - process: "MTDNA_SERVER_2:SAMPLE_REPORT"
          label: "Sample Report Generation"
          view: progressbar          
        - process: "MTDNA_SERVER_2:REPORT"
          label: "Dashboard Generation"
          view: progressbar
  inputs:

    - id: files
      description: Input Files
      type: local-folder
      pattern: "*.bam"

    - id: reference
      description: Reference
      type: list
      visible: false 
      value: "rcrs"
      values:
        "rcrs": "rCRS"

    - id: mode
      description: Mode
      type: list
      value: fusion
      values:
        mutserve: mutserve2 (SNV only)
        mutect2: mutect2  (SNV+INDEL)
        fusion: fusion (mutserve2 + mutect2)

    - id: detection_limit
      description: Detection Limit
      type: list
      value: 0.02
      values:
        0.01: 0.01
        0.02: 0.02        
        0.03: 0.03
        0.04: 0.04        
        0.05: 0.05
        0.1: 0.1      

    - id: coverage_estimation
      description: VAF Coverage Estimation
      type: list
      value: off
      values:
        on: On
        off: Off

    - id: subsampling
      description: Coverage Subsampling
      type: list
      value: on
      values:
        off: No subsampling
        on: Subsample to 2000x 

              
    - id: myseparator0
      type: separator

    - id: min_mean_coverage
      description: Minimal Mean Coverage 
      type: number
      visible: true
      value: 50  

    - id: baseQ
      description: Minimal Base Quality (Variant Calling)
      type: number
      visible: true 
      value: 20
      
    - id: mapQ
      description: Minimal Map Quality (Variant Calling)
      type: number
      visible: true
      value: 20      

  outputs:

    - id: output_reports
      description: Reports
      type: local-folder
      download: true
      temp: false

    - id: output
      description: Variants
      type: local-folder
      download: true
      temp: false

    - id: output_auxiliary
      description: Auxiliary Files
      type: local-folder
      download: true
      temp: false