preference-bigbed-workflow.cwl

#!/usr/bin/env cwl-runner
requirements:
- class: ScatterFeatureRequirement

class: Workflow
inputs:
  - id: "#tf1"
    type: string
  - id: "#tf1_bed_files"
    type:
      type: array
      items: File
  - id: "#tf1_threshold"
    type: float
  - id: "#tf2"
    type: string
  - id: "#tf2_threshold"
    type: float
  - id: "#tf2_bed_files"
    type:
      type: array
      items: File
  - id: "#intermediate_output_file_name"
    type: string
  - id: "#score_precision"
    type: int
    default: 2
  - id: "#assembly"
    type: string
  - id: "#output_bigbed_file_name"
    type: string
outputs:
  - id: "#output_file"
    type: File
    source: "#bed_to_bigbed.output_file"
  - id: "#output_bed_file"
    type: File
    source: "#add_itemrgb_column.output_file"
steps:
  - id: "#preferences"
    run: { import: predict-tf-preference.cwl }
    scatter:
      - "#preferences.tf1_bed_file"
      - "#preferences.tf2_bed_file"
    scatterMethod: dotproduct
    inputs:
    - { id: "#preferences.tf1", source: "#tf1" }
    - { id: "#preferences.tf2", source: "#tf2" }
    - { id: "#preferences.tf1_bed_file", source: "#tf1_bed_files" }
    - { id: "#preferences.tf2_bed_file", source: "#tf2_bed_files" }
    outputs:
    - { id: "#preferences.output_bed_file" }
  - id: "#threshold"
    run: { import: filter-tf-preference-threshold.cwl }
    scatter:
      - "#threshold.tf1_bed_file"
      - "#threshold.tf2_bed_file"
      - "#threshold.prefs_bed_file"
    scatterMethod: dotproduct
    inputs:
    - { id: "#threshold.tf1_bed_file", source: "#tf1_bed_files" }
    - { id: "#threshold.tf2_bed_file", source: "#tf2_bed_files" }
    - { id: "#threshold.prefs_bed_file", source: "#preferences.output_bed_file" }
    - { id: "#threshold.tf1_threshold", source: "#tf1_threshold" }
    - { id: "#threshold.tf2_threshold", source: "#tf2_threshold" }
    outputs:
    - { id: "#threshold.output_bed_file" }
  - id: "#combine"
    run: { import: combine-bed.cwl }
    inputs:
    - { id: "#combine.input_files", source: "#threshold.output_bed_file" }
    outputs:
    - { id: "#combine.output_file" }
  - id: "#sort"
    run: { import: sort-bed.cwl }
    inputs:
    - { id: "#sort.input_file", source: "#combine.output_file" }
    outputs:
    - { id: "#sort.output_file" }
  - id: "change_precision"
    run: { import: change-precision.cwl }
    inputs:
    - { id: "#change_precision.input_file", source: "#sort.output_file" }
    - { id: "#change_precision.precision", source: "#score_precision" }
    outputs:
    - { id: "#change_precision.output_file" }
  - id: "#add_itemrgb_column"
    run: { import: add-itemrgb-column.cwl }
    inputs:
    - { id: "#add_itemrgb_column.input_file", source: "#change_precision.output_file" }
    outputs:
    - { id: "#add_itemrgb_column.output_file" }
  - id: "#fetch_chrom_sizes"
    run: { import: fetch-chrom-sizes.cwl }
    inputs:
    - { id: "#fetch_chrom_sizes.assembly", source: "#assembly" }
    outputs:
    - { id: "#fetch_chrom_sizes.output_file" }
  - id: "#bed_to_bigbed"
    run: { import: bed-to-bigbed.cwl }
    inputs:
    - { id: "#bed_to_bigbed.input_file", source: "#add_itemrgb_column.output_file" }
    - { id: "#bed_to_bigbed.chrom_sizes_file", source: "#fetch_chrom_sizes.output_file" }
    - { id: "#bed_to_bigbed.output_file_name", source: "#output_bigbed_file_name" }
    outputs:
    - { id: "#bed_to_bigbed.output_file" }