As described in Creating New Workflow Bundles and Modules Using Maven Archetypes, new Java simplified workflow bundles are created through the mvn archetype:generate command and the com.github.seqware:seqware-archetype-java-workflow (SeqWare Java workflow archetype).
package net.sourceforge.seqware;
import java.util.Map;
import net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel;
import net.sourceforge.seqware.pipeline.workflowV2.model.Job;
import net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile;
public class WorkflowClient extends AbstractWorkflowDataModel {
@Override
public Map<String, SqwFile> setupFiles() {
SqwFile file0 = this.createFile("file_in_0");
file0.setSourcePath(this.getWorkflowBaseDir()+"/data/input.txt");
file0.setType("text/plain");
file0.setIsInput(true);
SqwFile file2 = this.createFile("file_in_1");
file2.setSourcePath(this.getWorkflowBaseDir()+"/data/input.txt");
file2.setType("text/plain");
file2.setIsInput(true);
SqwFile file3 = this.createFile("file_in_2");
file3.setSourcePath(this.getWorkflowBaseDir()+"/data/input1.txt");
file3.setType("text/plain");
file3.setIsInput(true);
SqwFile file1 = this.createFile("file_out");
file1.setSourcePath("dir2/output");
file1.setType("text/plain");
file1.setIsOutput(true);
file1.setForceCopy(true);
return this.getFiles();
}
@Override
public void setupDirectory() {
this.addDirectory("dir1");
this.addDirectory("dir2");
}
@Override
public void buildWorkflow() {
Job job00 = this.getWorkflow().createBashJob("bash_mkdir");
job00.getCommand().addArgument("mkdir test1");
Job job01 = this.getWorkflow().createPerlJob("perl_mkdir", this.getWorkflowBaseDir()+"/dependency/perltest.pl");
job01.getCommand().addArgument("test2");
Job job02 = this.getWorkflow().createBashJob("bash_mkdir");
job02.setCommand("mkdir test3");
Job job03 = this.getWorkflow().createBashJob("bash_mkdir");
job03.setCommand("mkdir test4");
Job job10 = this.getWorkflow().createBashJob("bash_cp");
job10.setCommand("cp " + this.getFiles().get("file_in_0").getProvisionedPath() + " test1");
job10.addParent(job00);
Job job11 = this.getWorkflow().createBashJob("bash_cp");
job11.setCommand("cp " + this.getFiles().get("file_in_1").getProvisionedPath() + " test2");
job11.addParent(job01);
Job job13 = this.getWorkflow().createBashJob("bash_cp");
job13.setCommand("cp " + this.getFiles().get("file_in_2").getProvisionedPath() + " test4");
job13.addParent(job03);
SqwFile fileout13 = new SqwFile();
fileout13.setIsOutput(true);
fileout13.setType("text/key-value");
fileout13.setSourcePath("test4/input1.txt");
fileout13.setForceCopy(true);
job13.addFile(fileout13);
Job job20 = this.getWorkflow().createBashJob("bash_cat");
job20.setCommand("cat test1/* test2/* > dir1/output_tmp");
job20.addParent(job10);
job20.addParent(job11);
SqwFile fileout = new SqwFile();
fileout.setIsOutput(true);
fileout.setType("text/key-value");
fileout.setSourcePath("dir1/output_tmp");
fileout.setForceCopy(true);
job20.addFile(fileout);
Job job30 = this.getWorkflow().createBashJob("bash_3");
SqwFile file = new SqwFile();
file.setIsInput(true);
file.setType("text/key-value");
file.setSourcePath(this.getWorkflowBaseDir()+"/data/input3.txt");
job30.addFile(file);
job30.getCommand().addArgument("cat " + file.getProvisionedPath() + " dir1/output_tmp > test3/input3" );
job30.addParent(job20);
job30.addParent(job02);
Job job31 = this.getWorkflow().createBashJob("bash_3");
job31.setCommand("cat test3/input3 > dir2/output");
job31.addParent(job20);
}
}
As described in Creating New Workflow Bundles and Modules Using Maven Archetypes, new FTL workflow bundles are created through the mvn archetype:generate command and the com.github.seqware:seqware-archetype-ftl-workflow (SeqWare FTL workflow archetype).
The following is a more complex example than that provided by the basic archetype generate command.
<workflow>
<files>
<file name="file_in_0" type="text/plain" forcecopy="false" sourcepath="${workflow_base_dir}/data/input.txt" input="true"/>
<file name="file_in_1" type="text/plain" forcecopy="false" sourcepath="${workflow_base_dir}/data/input.txt" input="true"/>
<file name="file_in_3" type="text/plain" forcecopy="false" sourcepath="${workflow_base_dir}/data/input1.txt" input="true"/>
<file name="file_out" type="text/plain" forcecopy="true" sourcepath="${workflow_base_dir}/dir2/output" input="false"/>
</files>
<dirs>
<dir>dir1</dir>
<dir>dir2</dir>
</dirs>
<jobs>
<job refid="ID000">
<algorithm>bash_mkdir</algorithm>
<argument>mkdir test1</argument>
</job>
<job refid="ID001" type="perl" script="${workflow_base_dir}/dependency/perltest.pl">
<algorithm>perl_mkdir</algorithm>
<argument>test2</argument>
</job>
<job refid="ID002">
<algorithm>bash_mkdir</algorithm>
<argument>mkdir test3</argument>
</job>
<job refid="ID003">
<algorithm>bash_mkdir</algorithm>
<argument>mkdir test4</argument>
</job>
<job refid="ID100">
<algorithm>bash_cp</algorithm>
<argument>cp ${workflow_base_dir}/data/input.txt test1</argument>
<parent>ID000</parent>
</job>
<job refid="ID101">
<algorithm>bash_cp</algorithm>
<argument>cp ${workflow_base_dir}/data/input.txt test2</argument>
<parent>ID001</parent>
</job>
<job refid="ID102">
<algorithm>bash_cp</algorithm>
<argument>cp ${workflow_base_dir}/data/input1.txt test3</argument>
<parent>ID002</parent>
<file name="file_out" type="text/plain" forcecopy="true" sourcepath="dir1/output13_tmp" input="false"/>
</job>
</jobs>
</workflow>