SBGWorkflow-class {sevenbridges} | R Documentation

## Build workflow

### Description

Build workflow

### Usage

    Flow(..., graph = TRUE, x.width = 1000, y.width = 400,
      x.start = 100, y.start = 200, canvas_zoom = 1, canvas_x = 40,
      canvas_y = 130)

    ## S4 method for signature 'Tool,Tool'
    e1 + e2

    ## S4 method for signature 'WorkflowStepList,Tool'
    e1 + e2

    ## S4 method for signature 'WorkflowStepList,WorkflowStepList'
    e1 + e2

    ## S4 method for signature 'App,App'
    e1 + e2

    ## S4 method for signature 'WorkflowStepList,App'
    e1 + e2

    e1 %>>% e2

    ## S4 method for signature 'Tool,Tool'
    e1 %>>% e2

    ## S4 method for signature 'Workflow,Tool'
    e1 %>>% e2

    ## S4 method for signature 'Workflow,Workflow'
    e1 %>>% e2

    ## S4 method for signature 'App,App'
    e1 %>>% e2

    ## S4 method for signature 'Workflow,App'
    e1 %>>% e2

### Arguments

`...` | extra arguments passed to SBGWorkflow
`graph` | if add graph coordinates or not, used for flow visualization on Seven Bridges platforms.
`x.width` | x scale width
`y.width` | y scale width
`x.start` | node x start point for a flow
`y.start` | node y start point for a flow
`canvas_zoom` | zoom factor
`canvas_x` | canvas x
`canvas_y` | canvas y
`e1` | either Tool App or Workflow object
`e2` | either Tool App or Workflow object

### Value

a SBGWorkflow object.

### Methods

`copy_obj()`

  this is a hack to make copy of reference cwl object

`get_input(ids, force = FALSE)`

  get input by pure input id from all steps

`get_input_exposed()`

  exposed input id other than file

`get_input_node()`

  get input file nodes id

`get_input_port()`

  show included port of all inputs

`get_output(ids, force = FALSE)`

  get output by pure output id from all steps

`get_output_node()`

  get output file nodes id

`get_required()`

  show flow required input id and types

`get_step(name = NULL, id = NULL)`

  get step object by name or id, name support pattern match

`get_tool(name = NULL, id = NULL)`

  get a tool object by name or id, name support pattern match

`input_id()`

  show input id

`input_matrix(new.order = c("id", "label", "type", "required", "prefix", "fileTypes"), required = NULL)`

  This return a matrix of input parameters, by default, following the order id, label, type, required, prefix, fileTypes. new.order accept names of column you want to print, but it has to be a field of inputs. When its set to NULL, it prints all fields. When required = TRUE, only print required field.

`input_type()`

  Show a vector of flow input type, names of them are input id.

`link_map()`

  show a table of all linked nodes

`linked_input_id()`

  input id that linked to an output

`linked_output_id()`

  output id that linked to an input

`list_tool()`

  list all tools included in this flow

`output_id()`

  show output id

`output_matrix(new.order = c("id", "label", "type", "fileTypes"))`

  This return a matrix of output parameters, by default, following the order id, label, type, fileTypes. new.order accept names of column you want to print, but it has to be a field of outputs. When its set to NULL, it prints all fields. When required = TRUE, only print required field.

`output_type()`

  Show a vector of flow output type, names of them are output id.

`run(run_inputs = list(), engine = c("bunny", "rabix", "cwlrun"))`

  Run this tool with inputs locally. Engines supported: bunny, rabix, cwlrun. Inputs accept list or JSON.

`set_batch(input = NULL, criteria = NULL, type = c("ITEM", "CRITERIA"))`

  Set a flow input node into a batch mode, this is now required before you execute a batch task on a batch-not-enabled flow.

`set_flow_input(iid = NULL, add = TRUE)`

  Expose tool input node as flow input, default is additative, if add = FALSE, this will overwrite and only made provided id inputs of flow.

`set_flow_output(oid = NULL, add = TRUE)`

  Expose tool output node as flow output, default is additative, if add = FALSE, this will overwrite and only made provided id outputs of flow.

`set_input_port(ids, include = TRUE)`

  set included port for provided input id(s)

`set_required(ids, required = TRUE)`

  Set a input node required (TRUE) or not required (FALSE) this require full input id (with tool id prefix) such as #STAR.alignIntronMax

`step_input_id(full = FALSE)`

  Show step input id, default names of them is tool id. When full = TRUE, show full name then names of vector is type.

`step_output_id(full = FALSE)`

  Show step output id, default names of them is tool id. when full = TRUE, show full name then names of vector is type.

### Examples

    f1 <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
    f1 <- convert_app(f1)
    # input matrix
    f1$input_matrix()
    # by name
    f1$input_matrix(c("id", "type", "required", "link_to"))
    # return only required
    f1$input_matrix(required = TRUE)
    # return everything
    f1$input_matrix(NULL)
    # return a output matrix with more informtion
    f1$output_matrix()
    # return only a few fields
    f1$output_matrix(c("id", "type"))
    # return everything
    f1$output_matrix(NULL)
    # flow inputs
    f1$input_type()
    # flow outouts
    f1$output_type()
    # flow input id
    f1$input_id()
    # linked input id
    f1$linked_input_id()
    # flow output id
    f1$output_id()
    # linked output id
    f1$linked_output_id()
    # link_map
    f1$link_map()
    # all step input id
    f1$step_input_id()
    # all step input full id with type
    f1$step_input_id(TRUE)
    # all step output id
    f1$step_output_id()
    # all step output full id with type
    f1$step_output_id(TRUE)
    # get inputs objects
    f1$get_input("#clip3pNbases")
    f1$get_input(c("#clip3pNbases", "#chimScoreMin"))
    f1$get_input(c("#clip3pNbases", "#chimScoreMin", "#STAR.outFilterMismatchNoverLmax"))
    # get outputs objects
    f1$get_output("#log_files")
    f1$get_output(c("#log_files", "intermediate_genome"))
    f1$get_output(c("#log_files", "intermediate_genome", "#STAR.unmapped_reads"))
    f1$get_output("#log_files")
    # set flow input
    f1$set_flow_input("#SBG_FASTQ_Quality_Detector.fastq")
    f1$set_flow_output(c("#log_files", "intermediate_genome"))
    # get required node
    f1$get_required()
    # set required node
    f1$steps[[1]]$run$set_required("genomeChrBinNbits")
    f1$get_required()
    f1$steps[[1]]$run$set_required("genomeChrBinNbits", FALSE)
    f1$get_required()
    # get Tool object from Flow by id and name
    f1$list_tool()
    # return two
    f1$get_tool("STAR")
    # return one
    f1$get_tool("^STAR$")
    # get included input ports
    f1$get_input_port()
    # set included input ports
    f1$set_input_port(c("#STAR.alignSJDBoverhangMin", "chimScoreSeparation"))
    f1$get_input_port()
    f1$set_input_port(c("#STAR.alignSJDBoverhangMin", "chimScoreSeparation"), FALSE)
    f1$get_input_port()
    f1$get_input_node()
    f1$get_output_node()
    f1$get_input_exposed()
    f1$step_input_id(TRUE)
    f1$input_id()
    f1$set_flow_input("#STAR.reads")
    f1$input_id()
    # batch
    f1$set_batch("sjdbGTFfile", c("metadata.sample_id", "metadata.library_id"))
    f1$set_batch("sjdbGTFfile", type = "ITEM")
    # add source to id
    f1$link_map()
    f1$add_source_to_id(c("test1", "test2"), c("#STAR.genome", "#STAR.reads"))
    f1$link_map()

[Package sevenbridges version 1.14.1 Index]