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

package BioX::Workflow::Command::inspect;

use v5.10;
use MooseX::App::Command;
use namespace::autoclean;

use Data::Dumper;
use YAML;
use Storable qw(dclone);
use Try::Tiny;
use JSON;

extends 'BioX::Workflow::Command';
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use Capture::Tiny ':all';

with 'BioX::Workflow::Command::run::Rules::Directives::Walk';
with 'BioX::Workflow::Command::run::Utils::Samples';
with 'BioX::Workflow::Command::run::Utils::Attributes';
with 'BioX::Workflow::Command::run::Rules::Rules';
with 'BioX::Workflow::Command::run::Utils::WriteMeta';
with 'BioX::Workflow::Command::run::Utils::Files::TrackChanges';
with 'BioX::Workflow::Command::run::Utils::Files::ResolveDeps';
with 'BioX::Workflow::Command::Utils::Files';

use BioX::Workflow::Command::run;
use BioX::Workflow::Command::inspect::Exceptions::Path;

command_short_description 'Inspect your workflow';
command_long_description
'Inspect individual variables in your workflow. Syntax is global.var for global, or rule.rulename.var for rules. Use the --all flag to inspect all variables.';

=head1 BioX::Workflow::Command::inspect

  biox inspect -h
  biox inspect -w variant_calling.yml --path /rules/.*/local/indir

=cut

=head2 Attributes

=cut

option 'all' => (
    is      => 'rw',
    isa     => 'Bool',
    default => 0,
);

option 'step_key' => (
    is      => 'rw',
    isa     => 'Bool',
    default => 0,
    documentation =>
'Type any key to continue to next rule key. Type \'q\' or \'quit\' to quit.',
);

option 'step_rule' => (
    is      => 'rw',
    isa     => 'Bool',
    default => 0,
    documentation =>
      'Type any key to continue to next rule. Type \'q\' or \'quit\' to quit.',
);

option 'path' => (
    is        => 'rw',
    isa       => 'Str',
    required  => 0,
    predicate => 'has_path',