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lib/BioX/Workflow/Plugin/Drake.pm  view on Meta::CPAN

Run the drake things

    drake --vars "SAMPLE=$sample" --workflow/workflow.drake

workflow.drake

    Our regular file

=cut

has 'min' => (
    is => 'rw',
    isa => 'Bool',
    default => 0,
);

=head2 Subroutines

Subroutines

=head3 before run

Must initialize some variables

=cut

before 'run' => sub{
    my($self) = shift;

    if($self->min){
        $self->full(0);
    }
    $self->wait(0);
    $self->comment_char(';');
};

=head3 after get_samples

Things to do if we decide to do a min version

=cut

after 'get_samples' => sub{
    my($self) = shift;

    return unless $self->min;

    open(my $fh, '>', 'run-workflow.sh') or die print "Could not open file $!\n";

    print $fh "#!/bin/bash\n\n";

    foreach my $sample (@{$self->samples}){
        print $fh <<EOF;
drake --vars "SAMPLE=$sample" --workflow workflow.drake
EOF
    }

    close $fh;

    chmod 0777, 'run-workflow.sh';

    $self->samples(["\$SAMPLE"]);
};

=head3 write_process

Fill in the template with the process

Ensure INPUT/OUTPUT exist

Prettyify the output a bit

=cut

before 'write_process' => sub{
    my($self) = shift;

    $DB::single=2;
    if((! $self->local_attr->exists('INPUT')) && ! $self->local_attr->exists('OUTPUT') ){
        print "$self->{comment_char} There is no INPUT or OUTPUT!\n";
    }

    #Make the formatting a big prettier
    my @tmp = split("\n", $self->process);
    $self->process(join("\n\t", @tmp));

    my $tmp = "{\$self->OUTPUT} <- {\$self->INPUT}\n\t";
    $DB::single=2;
    if($self->min){
        $tmp =~ s/\$SAMPLE/\$[SAMPLE]/g;
    }
    my $newprocess = $tmp.$self->process;
    $self->process($newprocess);
};

#before 'process_template' => sub {
    #my $self = shift;

    #my $tmp = "{\$self->OUTPUT} <- {\$self->INPUT}\n\t";
    #$DB::single=2;
    #if($self->min){
        #$tmp =~ s/\$SAMPLE/\$[SAMPLE]/g;
    #}
    #my $newprocess = $tmp.$self->process;
    #$self->process($newprocess);

#};

1;
__END__

=encoding utf-8

=head1 AUTHOR

Jillian Rowe E<lt>jillian.e.rowe@gmail.comE<gt>

=head1 COPYRIGHT

Copyright 2015- Jillian Rowe