disconnect

Import the pipeline and block objects needed for the example.

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

Create a pipeline.

P = Pipeline;

Create two FileChooser blocks and a Bowtie2 block. The files represent pair-end read data for the Drosophila genome. These read files are already provided with the toolbox.

reads1 = FileChooser(which("SRR6008575_10k_1.fq"));
reads2 = FileChooser(which("SRR6008575_10k_2.fq"));
bowtie2Block = Bowtie2;

Add the blocks. Define the block names as "reads1","reads2", and "bowtie2" and add them in the same call.

addBlock(P,[reads1,reads2,bowtie2Block],["reads1","reads2","bowtie2"]);

Check the names of the output and input ports of the blocks to connect.

reads1.Outputs

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

reads2.Outputs

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

bowtie2Block.Inputs

ans = struct with fields:
    IndexBaseName: [1×1 bioinfo.pipeline.Input]
      Reads1Files: [1×1 bioinfo.pipeline.Input]
      Reads2Files: [1×1 bioinfo.pipeline.Input]

The Bowtie2 block has two required and one optional inputs. Set the value of the first required input IndexBaseName to "Dmel_chr4", which is the base name for the reference index files, which are provided with the toolbox, for the Drosophila genome.

bowtie2Block.Inputs.IndexBaseName.Value = "Dmel_chr4";

Because you are providing the pair-end (paired) read data, connect Reads1Files to the Files output of the reads1 block, which contains the first mate reads "SRR6008575_10k_1.fq" and connect Reads2Files to the reads2 block that contains the second mate reads "SRR6008575_10k_2.fq". The Reads2Files input is optional and is not needed if you have the single-end (unpaired) read data.

connect(P,reads1,bowtie2Block,["Files","Reads1Files"]);
connect(P,reads2,bowtie2Block,["Files","Reads2Files"]);

Run the pipeline.

run(P);

The Bowtie2 block generates a SAM file as the output.

mappedReads = results(P,bowtie2Block)

mappedReads = struct with fields:
    SAMFile: [1×1 bioinfo.pipeline.datatype.File]

Suppose you want to provide a single end read data to the bowtie2Block. You can update the reads1 block to read in such a single end read file and disconnect the Reads2File optional input of bowtie2Block. The disconnect function returns an empty string array, which means that there are no more connection between two blocks.

reads1.Files = which("SRR005164_1_50.fastq");
disconnect(P,reads2,bowtie2Block,["Files","Reads2Files"])

ans = 

  0×2 empty string array

Alternatively, you can use portMap to check if there are any connections between two blocks.

portMap(P,reads2,bowtie2Block)

ans = 

  0×2 empty string array

You can then run the pipeline again.

run(P);
mappedReads = results(P,bowtie2Block)

mappedReads = struct with fields:
    SAMFile: [1×1 bioinfo.pipeline.datatype.File]