link: link two nodes to form a new Workflow

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

Description

link two nodes to form a new Workflow

Usage

link(from, to, ...)

## S4 method for signature 'Tool,Tool'
link(
  from,
  to,
  id1,
  id2,
  flow_id = NULL,
  flow_label = NULL,
  flow_input = NULL,
  flow_output = NULL
)

## S4 method for signature 'Tool,Workflow'
link(
  from,
  to,
  id1,
  id2,
  flow_id = NULL,
  flow_label = NULL,
  flow_input = NULL,
  flow_output = NULL
)

## S4 method for signature 'Workflow,Tool'
link(
  from,
  to,
  id1,
  id2,
  flow_id = NULL,
  flow_label = NULL,
  flow_input = NULL,
  flow_output = NULL
)

## S4 method for signature 'Workflow,Workflow'
link(from, to, id1, id2)

## S4 method for signature 'App,ToolORWorkflow'
link(from, to, id1, id2)

## S4 method for signature 'ToolORWorkflow,App'
link(from, to, id1, id2)

Arguments

from	either Tool App or Workflow object
to	either Tool App or Workflow object
...	more auguments
id1	id to be connected from the ouput of the first node
id2	id id to be connected from the input of the second first node
flow_id	workflow id, if ignored, going to create one by joning tool id.
flow_label	workflow label, if ignored, going to create one by joning tool labels.
flow_input	full flow input id, e.g. "#SBG_Unpack_FASTQs.input_archive_file"
flow_output	full flow output id, e.g. "#STAR.log_files"

Details

Flexible enought to allow users to connect two objects by ids

Value

A Workflow object

Examples

t1 <- system.file("extdata/app", "tool_unpack_fastq.json", package = "sevenbridges")
t2 <- system.file("extdata/app", "tool_star.json", package = "sevenbridges")
t1 <- convert_app(t1)
t2 <- convert_app(t2)
# check possible link
link_what(t1, t2)
# link
f1 <- link(t1, t2, "output_fastq_files", "reads")
# link
f2 <- link(
  t1, t2, "output_fastq_files", "reads",
  flow_input = "#SBG_Unpack_FASTQs.input_archive_file",
  flow_output = "#STAR.log_files"
)

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