portMap

Import the Pipeline and block objects needed for the example.

import bioinfo.pipeline.Pipeline
import bioinfo.pipeline.block.*

Create a pipeline.

qcpipeline = Pipeline;

Select an input FASTQ file using a FileChooser block.

fastqfile = FileChooser(which("SRR005164_1_50.fastq"));

Create a SeqFilter block.

sequencefilter = SeqFilter;

Add blocks to the pipeline. Optionally, you can specify the block names.

addBlock(qcpipeline,[fastqfile,sequencefilter],["FF","SF"]);

Connect the output of the first block to the input of the second block. To do so, you need to first check the input and output port names of the corresponding blocks.

View the Outputs (port of the first block) and Inputs (port of the second block).

fastqfile.Outputs

ans = struct with fields:
    Files: [1×1 bioinfo.pipeline.Output]

sequencefilter.Inputs

ans = struct with fields:
    FASTQFiles: [1×1 bioinfo.pipeline.Input]

Connect the Files output port of the fastqfile block to the FASTQFiles port of sequencefilter block. The output is a 1-by-2 string array, indicating the names of two ports that are now connected. You can use either the block objects themselves or the block names that you have defined previously. The next command uses the block names to identify and connect these two blocks.

connectedports = connect(qcpipeline,"FF","SF",["Files","FASTQFiles"])

connectedports = 1×2 string
    "Files"    "FASTQFiles"

You can also query the names of connected ports using portMap.

portnames = portMap(qcpipeline,"FF","SF")

portnames = 1×2 string
    "Files"    "FASTQFiles"