compress_pipeline.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: Workflow
label: compress_pipeline

requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement

inputs:
- id: flag_autocorrelation
  type: boolean?
- id: is_long_baseline
  type: boolean?
- id: msin
  type: Directory

outputs:
- id: inspect
  type: File
  outputSource:
  - inspect_step/inspect_file
- id: logfile
  type: File[]?
  outputSource:
  - dppp/logfile
- id: compressed
  type: File?
  outputSource:
  - compress/compressed
- id: ingest
  type: Any?
  outputSource:
  - format_ingest/ingest
- id: applied_fixes
  type: string[]
  outputSource:
  - identify_issues/issue_list
- id: unfixable_issues
  type: string[]
  outputSource:
  - identify_issues/unfixable_issues
- id: keep_input
  type: boolean
  outputSource: identify_issues/skip_compress
- id: input_storage_manager
  type: string
  outputSource: identify_issues/input_storage_manager

steps:
- id: identify_issues
  in:
  - id: msin
    source: msin
  - id: is_long_baseline
    source: is_long_baseline
  run: steps/identify_issues.cwl
  out:
  - issue_list
  - is_raw
  - unfixable_issues
  - msout
  - skip_compress
  - input_storage_manager
- id: fix_ai_2013
  in:
  - id: msin
    source: identify_issues/msout