link two nodes to form a new Workflow

Usage

link(from, to, ...)

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

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

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

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

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

# S4 method for 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"

Value

A Workflow object

Details

Flexible enought to allow users to connect two objects by ids

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)
#> $File...
#> $File...$from
#>                    id              label    type fileTypes          full.name
#> 1 #output_fastq_files Output FASTQ files File...     FASTQ #SBG_Unpack_FASTQs
#> 
#> $File...$to
#>              id                label    type required prefix
#> 1        #reads        Read sequence File...     TRUE   <NA>
#> 95 #sjdbGTFfile Splice junction file File...    FALSE   <NA>
#>                                                   fileTypes full.name
#> 1  FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2     #STAR
#> 95                                            GTF, GFF, TXT     #STAR
#> 
#> 
# link
f1 <- link(t1, t2, "output_fastq_files", "reads")
#> flow_input: #SBG_Unpack_FASTQs.input_archive_file / #STAR.sjdbGTFfile / #STAR.genome
#> flow_output: #STAR.aligned_reads / #STAR.transcriptome_aligned_reads / #STAR.reads_per_gene / #STAR.log_files / #STAR.splice_junctions / #STAR.chimeric_junctions / #STAR.unmapped_reads / #STAR.intermediate_genome / #STAR.chimeric_alignments
# link
f2 <- link(
  t1, t2, "output_fastq_files", "reads",
  flow_input = "#SBG_Unpack_FASTQs.input_archive_file",
  flow_output = "#STAR.log_files"
)
#> flow_input: #SBG_Unpack_FASTQs.input_archive_file / #STAR.genome
#> flow_output: #STAR.log_files