MitoZ.yaml 1.66 KB
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{
  name: MitoZ,
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  docker_name: mitoz,
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  description: ,
  version: "0.0.1",
  author: "MBB",
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  input: raw_reads,
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  steps:
    [
      { title: Trimming, name: trimming, tools: [cutadapt, "null"], default: "null" },
      { title: Filter, name: filter, tools: [mitoz_filter,"null"], default: mitoz_filter},
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      { title: Assemble, name: assemble, tools: [mitoz_assemble], default: mitoz_assemble}, # Runs mitoz_findmitoscaf after assembling
      #{ title: Find Mito scaffold, name: findmitoscaf, tools: [mitoz_findmitoscaf], default: mitoz_findmitoscaf},
      { title: Annotate, name: annotate, tools: [mitoz_annotate], default: mitoz_annotate}, # Runs mitoz_visualize after annotating
      { title: Visualize, name: visualize, tools: [igv_visualize], default: igv_visualize },
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    ],
  options:
    [
      {
        name: "results_dir",
        type: "output_dir",
        value: "/Results",
        label: "Results directory: ",
        volumes:  [Results: "/Results"]
      },
      {
        name: "sample_dir",
        type: "input_dir",
        value: "/Data",
        label: "Data directory: ",
        volumes:  [Data: "/Data", Results: "/Results"]
      },
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      #{
      #  name: "sample_suffix",
      #  type: "text",
      #  value: ".fastq.gz",
      #  label: "Samples suffix: ",
      #},
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      {
        name: "SeOrPe",
        type: "radio",
        value: "PE",
        choices: [Single end: SE, Paired end: PE],
        label: "Single end reads (SE) or Paired end reads (PE): ",
      },
    ],
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    params_equals: [
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      { param_A: mitoz_findmitoscaf_clade, param_B: mitoz_assemble_clade },
      { param_A: mitoz_findmitoscaf_clade, param_B: mitoz_annotate_clade },
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    ]
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}