fpfilter-tool/fpfilter.cwl at master · OpenGenomics/fpfilter-tool · GitHub

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class: CommandLineTool
label: fpfilter
cwlVersion: v1.0
baseCommand: ["perl", "/opt/fpfilter.pl"]
requirements:
  - class: DockerRequirement
    dockerPull: opengenomics/fpfilter:latest
inputs:
  vcf-file:
    type: File
    label: the input VCF file. Must have a GT field.
    inputBinding:
      prefix: --vcf-file
  bam-file:
    type: File
    label: the BAM file of the sample you are filtering on. Typically the tumor.
    inputBinding:
      prefix: --bam-file
    secondaryFiles:
      - .bai
  sample:
    type: string
    label: The sample name of the sample you want to filter on in the VCF file.
    default: "TUMOR"
    inputBinding:
      prefix: --sample
  reference:
    type: File
    label: a fasta containing the reference sequence the BAM file was aligned to.
    inputBinding:
      prefix: --reference
  min-read-pos:
    type: float
    label: minimum average relative distance from start/end of read
    default: 0.10
    inputBinding:
      prefix: --min-read-pos
  min-var-freq:
    type: float
    default: 0.05
    label: minimum variant allele frequency
    inputBinding:
      prefix: --min-var-freq
  min-var-count:
    type: int
    label: minimum number of variant-supporting reads
    default: 3
    inputBinding:
      prefix: --min-var-count
  min-strandedness:
    type: float
    default: 0.01
    label: minimum representation of variant allele on each strand
    inputBinding:
      prefix: --min-strandedness
  max-mm-qualsum-diff:
    type: int
    default: 50
    label: maximum difference of mismatch quality sum between variant and reference reads (paralog filter)
    inputBinding:
      prefix: --max-mm-qualsum-diff
  max-var-mm-qualsum:
    type: int
    label: maximum mismatch quality sum of reference-supporting reads
    default: 100
    inputBinding:
      prefix: --max-var-mm-qualsum
  max-mapqual-diff:
    type: int
    label: maximum difference of mapping quality between variant and reference reads
    default: 30
    inputBinding:
      prefix: --max-mapqual-diff
  max-readlen-diff:
    type: int
    label: maximum difference of average supporting read length between variant and reference reads (paralog filter)
    default: 25
    inputBinding:
      prefix: --max-readlen-diff
  min-var-dist-3:
    type: float
    label: 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
  output:
    type: string
    default: filtered.vcf
    inputBinding:
      prefix: --output

outputs:
  filtered_vcf:
    type: File
    outputBinding:
      glob: $(inputs.output)