Pack a CWL workflow and output a file

Pack a CWL workflow and output a file

pack_to_file(input, output)

Arguments

input	Path to the input CWL file
output	Path to the output CWL file

Examples

input <- system.file("example/remote-cwl/wf1.cwl", package = "sbpack")
output <- tempfile(fileext = ".cwl")
pack_to_file(input, output)
cat(readLines(output), sep = "\n")
#> class: Workflow
#> cwlVersion: v1.0
#> inputs:
#> - id: in1
#>   type: {items: boolean, label: A boolean array, name: my_boolean_array, type: array}
#> outputs:
#> - {id: out1, outputSource: s2/out1, type: string}
#> requirements:
#>   InlineJavascriptRequirement: {}
#>   SubworkflowFeatureRequirement: {}
#> steps:
#>   s1:
#>     in: {in1: in1}
#>     out: [out1]
#>     run:
#>       arguments:
#>       - {valueFrom: $(runtime)}
#>       baseCommand: echo
#>       class: CommandLineTool
#>       cwlVersion: v1.0
#>       inputs:
#>         in1:
#>           inputBinding: {position: 1, valueFrom: 'A_$(inputs.in1)_B_${return inputs.in1}_C_$(inputs.in1)'}
#>           type: {items: boolean, label: A boolean array, name: my_boolean_array, type: array}
#>       outputs:
#>         out1:
#>           outputBinding: {glob: out.txt, loadContents: true, outputEval: $(self)_D_$(runtime)}
#>           type: string
#>       requirements:
#>         InlineJavascriptRequirement: {}
#>       stdout: out.txt
#>   s2:
#>     in: {in1: s1/out1}
#>     out: [out1]
#>     run:
#>       arguments:
#>       - {valueFrom: $(runtime)}
#>       baseCommand: echo
#>       class: CommandLineTool
#>       cwlVersion: v1.0
#>       inputs:
#>         in1:
#>           inputBinding: {position: 1, valueFrom: 'A_$(inputs.in1)_B_${return inputs.in1}_C_$(inputs.in1)'}
#>           type: string
#>       outputs:
#>         out1:
#>           outputBinding: {glob: out.txt, loadContents: true, outputEval: $(self)_D_$(runtime)}
#>           type: string
#>       requirements:
#>         InlineJavascriptRequirement:
#>           expressionLib: ["var foo = function(x) {\n    return 2 * x\n}\n\nvar bar
#>               = function(n, x) {\n    return `{n} engineers walk into a {x}`\n}"]
#>       stdout: out.txt

input <- "https://raw.githubusercontent.com/rabix/sbpack/master/tests/wf2.cwl"
output <- tempfile(fileext = ".cwl")
pack_to_file(input, output)
cat(readLines(output), sep = "\n")
#> class: Workflow
#> cwlVersion: v1.0
#> inputs:
#>   in1:
#>     type: {items: boolean, label: A boolean array, name: my_boolean_array, type: array}
#>   in2:
#>     type:
#>       label: A required enum
#>       name: my_enum
#>       symbols: [a, b, c]
#>       type: enum
#> outputs:
#>   out1: {outputSource: s2/out1, type: string}
#> requirements:
#>   InlineJavascriptRequirement: {}
#>   SubworkflowFeatureRequirement: {}
#> steps:
#>   s1:
#>     in:
#>     - {id: in1, source: in1}
#>     out: [out1]
#>     run:
#>       class: Workflow
#>       cwlVersion: v1.0
#>       inputs:
#>       - id: in1
#>         type: {items: boolean, label: A boolean array, name: my_boolean_array, type: array}
#>       outputs:
#>       - {id: out1, outputSource: s2/out1, type: string}
#>       requirements:
#>         InlineJavascriptRequirement: {}
#>         SubworkflowFeatureRequirement: {}
#>       steps:
#>         s1:
#>           in: {in1: in1}
#>           out: [out1]
#>           run:
#>             arguments:
#>             - {valueFrom: $(runtime)}
#>             baseCommand: echo
#>             class: CommandLineTool
#>             cwlVersion: v1.0
#>             inputs:
#>               in1:
#>                 inputBinding: {position: 1, valueFrom: 'A_$(inputs.in1)_B_${return
#>                     inputs.in1}_C_$(inputs.in1)'}
#>                 type: {items: boolean, label: A boolean array, name: my_boolean_array,
#>                   type: array}
#>             outputs:
#>               out1:
#>                 outputBinding: {glob: out.txt, loadContents: true, outputEval: $(self)_D_$(runtime)}
#>                 type: string
#>             requirements:
#>               InlineJavascriptRequirement: {}
#>             stdout: out.txt
#>         s2:
#>           in: {in1: s1/out1}
#>           out: [out1]
#>           run:
#>             arguments:
#>             - {valueFrom: $(runtime)}
#>             baseCommand: echo
#>             class: CommandLineTool
#>             cwlVersion: v1.0
#>             inputs:
#>               in1:
#>                 inputBinding: {position: 1, valueFrom: 'A_$(inputs.in1)_B_${return
#>                     inputs.in1}_C_$(inputs.in1)'}
#>                 type: string
#>             outputs:
#>               out1:
#>                 outputBinding: {glob: out.txt, loadContents: true, outputEval: $(self)_D_$(runtime)}
#>                 type: string
#>             requirements:
#>               InlineJavascriptRequirement:
#>                 expressionLib: ["var foo = function(x) {\n    return 2 * x\n}\n\nvar
#>                     bar = function(n, x) {\n    return `{n} engineers walk into a
#>                     {x}`\n}"]
#>             stdout: out.txt
#>   s2:
#>     in: {in1: s1/out1}
#>     out: [out1]
#>     run:
#>       arguments:
#>       - {valueFrom: $(runtime)}
#>       baseCommand: echo
#>       class: CommandLineTool
#>       cwlVersion: v1.0
#>       inputs:
#>         in1:
#>           inputBinding: {position: 1, valueFrom: 'A_$(inputs.in1)_B_${return inputs.in1}_C_$(inputs.in1)'}
#>           type: string
#>       outputs:
#>         out1:
#>           outputBinding: {glob: out.txt, loadContents: true, outputEval: $(self)_D_$(runtime)}
#>           type: string
#>       requirements:
#>         InlineJavascriptRequirement:
#>           expressionLib: ["var foo = function(x) {\n    return 2 * x\n}\n\nvar bar
#>               = function(n, x) {\n    return `{n} engineers walk into a {x}`\n}"]
#>       stdout: out.txt