deleteResults

Import the pipeline and block objects needed for the example.

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

Create a pipeline.

P = Pipeline;

Create FileChooser and SamSort blocks.

FCB = FileChooser(which("ex1.sam"));
SSB = SamSort;

Add blocks to the pipeline. You can pass in the names of the blocks ("myFileChooser" and "mySamSorter") and connect them.

addBlock(P,[FCB, SSB],["myFileChooser","mySamSorter"]);
connect(P, FCB, SSB, ["Files","SAMFile"]);

Run the pipeline.

run(P,ResultsDirectory="C:\Examples\")

Check the results. During the pipeline run, the pipeline created a folder for each block with the same name as the block name. In this case, the pipeline created myFileChooser and mySamSorter folders in the above results directory C:\Examples. Each block results folder can contain 1 to N number of folders determined by the number of times a block processes in a given run. In this case, each block is processed just one time and the block results folder contains a subfolder named "1" that has the block results.

Set Expanded to true to expand the table variable values which are cell arrays.

tbl = processTable(P,Expanded=true)

tbl=2×5 table
         Block          Status            RunStart                 RunEnd              RunErrors    
    _______________    _________    ____________________    ____________________    ________________

    "myFileChooser"    Completed    26-Jul-2023 09:02:06    26-Jul-2023 09:02:06    {0×0 MException}
    "mySamSorter"      Completed    26-Jul-2023 09:02:06    26-Jul-2023 09:02:06    {0×0 MException}

Check the result of the SamSort block. It indicates the output of the block is a sorted SAM file.

r = results(P,SSB)

r = struct with fields:
    SortedSAMFile: [1×1 bioinfo.pipeline.datatype.File]

Check the full file path of the sorted file.

unwrap(r.SortedSAMFile)

ans = 
"C:\Examples\mySamSorter\1\ex1.sorted.sam"

Delete the SamSort block result from the pipeline. After deletion, the SAM file output value is now incomplete.

deleteResults(P,SSB)
r = results(P,SSB)

r = 
  Incomplete pipeline result.

However, the generated directory (mySamSorter) and actual SAM file still exists in that directory. To delete them also from your computer completely, use IncludeFiles name-value argument.

deleteResults(P,SSB,IncludeFiles=true)