Flow: Build workflow

In sbg/sevenbridges-r: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

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()

sbg/sevenbridges-r documentation built on March 26, 2021, 3:33 p.m.