fpfilter.cwl.yaml

class: CommandLineTool
label: fpfilter
baseCommand: [perl, /opt/fpfilter.pl, --output, fpfilter.vcf]
requirements:
  - class: "DockerRequirement"
    dockerImageId: "opengenomics/fpfilter:0.0.1"
inputs:
  - id: "#vcf-file"
    type: File
    description: the input VCF file. Must have a GT field.
    inputBinding:
      prefix: --vcf-file
  - id: "#bam-file"
    type: File
    description: the BAM file of the sample you are filtering on. Typically the tumor.
    inputBinding:
      prefix: --bam-file
      secondaryFiles:
        - .bai
  - id: "#sample"
    type: string
    description: The sample name of the sample you want to filter on in the VCF file.
    default: "TUMOR"
    inputBinding:
      prefix: --sample
  - id: "#reference"
    type: File
    description: a fasta containing the reference sequence the BAM file was aligned to.
    inputBinding:
      prefix: --reference
  - id: "#output"
    type: File
    inputBinding:
      prefix: --output
  - id: "#min-read-pos"
    type: float
    description: minimum average relative distance from start/end of read
    default: 0.10
    inputBinding:
      prefix: --min-read-pos
  - id: "#min-var-freq"
    type: float
    default: 0.05
    default: minimum variant allele frequency
    inputBinding:
      prefix: --min-var-freq
  - id: "#min-var-count"
    type: integer
    description: minimum number of variant-supporting reads
    default: 4
    inputBinding:
      prefix: --min-var-count
  - id: "#min-strandedness"
    type: float
    default: 0.01
    description: minimum representation of variant allele on each strand
    inputBinding:
      prefix: --min-strandedness
  - id: "#max-mm-qualsum-diff"
    type: integer
    default: 50
    description: maximum difference of mismatch quality sum between variant and reference reads (paralog filter)
    inputBinding:
      prefix: --max-mm-qualsum-diff
  - id: "#max-var-mm-qualsum"
    type: integer
    description: maximum mismatch quality sum of reference-supporting reads
    default: 100
    inputBinding:
      prefix: --max-var-mm-qualsum
  - id: "#max-mapqual-diff"
    type: integer
    description: maximum difference of mapping quality between variant and reference reads
    default: 30
    inputBinding:
      prefix: --max-mapqual-diff
  - id: "#max-readlen-diff"
    type: integer
    description: maximum difference of average supporting read length between variant and reference reads (paralog filter)
    default: 25
    inputBinding:
      prefix: --max-readlen-diff
  - id: "#min-var-dist-3"
    type: integer
    description: minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads
    default: 0.20
    inputBinding:
      prefix: --min-var-dist-3
  - id: "#output"
    type: string
    default: filtered.vcf
    inputBinding:
      prefix: --output
  
outputs:
  - id: "output"
    type: File
    outputBinding:
      glob:
        engine: "cwl:JsonPointer"
        script: job/output