link two nodes to form a new Workflow

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