SBGWorkflow-class {sevenbridges} | R Documentation |
Build workflow
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
... |
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 |
a SBGWorkflow object.
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.
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()