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lib/BioX/Workflow/Command/Utils/Files.pm  view on Meta::CPAN

package BioX::Workflow::Command::Utils::Files;

use MooseX::App::Role;
use namespace::autoclean;

use MooseX::Types::Path::Tiny qw/AbsFile/;
use File::Basename;
use DateTime;
use Try::Tiny;
use Config::Any;
use File::Spec;

option 'workflow' => (
    is            => 'rw',
    isa           => AbsFile,
    required      => 1,
    coerce        => 1,
    documentation => 'Supply a workflow',
    cmd_aliases   => ['w'],
);

=head3 workflow_data

initial config file read into a perl structure

=cut

has 'workflow_data' => (
    is      => 'rw',
    isa     => 'HashRef',
    default => sub { return {} },
);

option 'outfile' => (
    is      => 'rw',
    isa     => 'Str',
    lazy    => 1,
    default => sub {
        my $self     = shift;
        my $workflow = $self->workflow;
        my @files    = fileparse( $self->workflow, qr/\.[^.]*/ );
        my $dt       = DateTime->now( time_zone => 'local' );
        my $file_name =
          $files[0] . '_' . $dt->ymd . '_' . $dt->time('-') . '.sh';
        return File::Spec->rel2abs( $file_name );
    },
    documentation => 'Write your workflow to a file',
    cmd_aliases   => ['o'],
);

option 'stdout' => (
    is            => 'rw',
    isa           => 'Bool',
    default       => 0,
    documentation => 'Write workflows to STDOUT',
    predicate     => 'has_stdout',
);

has 'fh' => (
    is      => 'rw',
    lazy    => 1,
    default => sub {
        my $self = shift;
        my $fh   = new IO::File;
        if ( $self->stdout ) {
            $fh->fdopen( fileno(STDOUT), "w" );
        }
        else {
            $fh->open( "> " . $self->outfile );