An example workflow on TGI's GMS.

workflow_example.pm

sub _run_workflow {
  my $self = shift;
  my $lsf_queue = $ENV{GENOME_LSF_QUEUE_BUILD_WORKER_ALT};
  my $lsf_project = 'varscan_filter';
 
  my $w = Workflow::Operation->create(
    name => "Filter Varscan SNVs",
    operation_type => Workflow::OperationType::Command->get(
      'Genome::Model::Tools::Capture::FormatSnvs')
  );
  $w->parallel_by('variants_file');
  $w->log_dir("/gscmnt/gc2607/mardiswilsonlab/aramu/test/genome/lib/perl/Genome/Model/Tools/Varscan");

  # Validate the workflow
  my @errors = $w->validate;
  if (@errors) {
    $self->error_message(@errors);
    die "Errors validating workflow\n";
  }

  # the hardcoding here is just for example.
  $self->status_message("Launching workflow now.");
  my @inputs1 = (
    "/gscmnt/gc2607/mardiswilsonlab/aramu/analysis/misc/loh/PNS1_loh/varscan.snps.1.snp",
    "/gscmnt/gc2607/mardiswilsonlab/aramu/analysis/misc/loh/PNS1_loh/varscan.snps.2.snp");
  my @outputs = ("tmp", "tmp2");
  print \@inputs1;
  # Launch workflow
  my $result = Workflow::Simple::run_workflow_lsf(
    $w,
    'variants_file' => \@inputs1,
    'output_file' => \@outputs,
  );

  #Collect and analyze results
  unless($result){
    foreach my $error (@Workflow::Simple::ERROR) {
      $self->error_message($error->stdout());
      $self->error_message($error->stderr());
    }
    die $self->error_message("Workflow did not return correctly.");
  }
  return 1;
}