+ steps:
+ - id: main_2_embed_1
+ in:
+ fed_migrate:
+ source: fed_migrate
+ host:
+ source: host
+ token:
+ source: token
+ out:
+ - report
+ run:
+ arguments:
+ - $(inputs.fed_migrate)
+ - '--report'
+ - report.csv
+ class: CommandLineTool
+ id: main_2_embed_1_embed
+ inputs:
+ - id: fed_migrate
+ type: string
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ outputs:
+ - id: report
+ outputBinding:
+ glob: report.csv
+ type: File
+ requirements:
+ InlineJavascriptRequirement: {}
+ - id: main_2_embed_2
+ in:
+ host:
+ source: host
+ report:
+ source: main_2_embed_1/report
+ token:
+ source: token
+ out:
+ - report2
+ run:
+ arguments:
+ - sed
+ - '-E'
+ - 's/,(case[1-8])2?,/,\1,/g'
+ class: CommandLineTool
+ id: main_2_embed_2_embed
+ inputs:
+ - id: report
+ type: File
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ outputs:
+ - id: report2
+ outputBinding:
+ glob: report.csv
+ type: File
+ requirements:
+ InlineJavascriptRequirement: {}
+ stdin: $(inputs.report.path)
+ stdout: report.csv
+ - id: main_2_embed_3
+ in:
+ fed_migrate:
+ source: fed_migrate
+ host:
+ source: host
+ report2:
+ source: main_2_embed_2/report2
+ token:
+ source: token
+ out:
+ - report3
+ run:
+ arguments:
+ - $(inputs.fed_migrate)
+ - '--migrate'
+ - $(inputs.report2)
+ class: CommandLineTool
+ id: main_2_embed_3_embed
+ inputs:
+ - id: report2
+ type: File
+ - id: fed_migrate
+ type: string
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ outputs:
+ - id: report3
+ outputBinding:
+ outputEval: $(inputs.report2)
+ type: File
+ requirements:
+ InlineJavascriptRequirement: {}
+ - id: main_2_embed_4
+ in:
+ arvados_api_hosts:
+ source: arvados_api_hosts
+ check:
+ default:
+ class: File
+ location: check.py
+ host:
+ source: host
+ report3:
+ source: main_2_embed_3/report3
+ superuser_tokens:
+ source: superuser_tokens
+ token:
+ source: token
+ out:
+ - r
+ run:
+ arguments:
+ - python
+ - $(inputs.check)
+ - _script
+ class: CommandLineTool
+ id: main_2_embed_4_embed
+ inputs:
+ - id: report3
+ type: File
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ - id: arvados_api_hosts
+ type:
+ items: string
+ type: array
+ - id: superuser_tokens
+ type:
+ items: string
+ type: array
+ - id: check
+ type: File
+ outputs:
+ - id: r
+ outputBinding:
+ outputEval: $(inputs.report3)
+ type: File
+ requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entry: |
+ {
+ "arvados_api_hosts": $(inputs.arvados_api_hosts),
+ "superuser_tokens": $(inputs.superuser_tokens)
+ }
+ entryname: _script
+ InlineJavascriptRequirement: {}