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lib/BioX/Workflow/Command/run/Rules/Directives/Sample.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Rules::Directives::Sample;

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

use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use MooseX::Types::Path::Tiny qw/Path Paths AbsPath AbsPaths AbsFile/;

=head3 sample_rule

Rule to find files/samples

=cut

has 'sample_rule' => (
    is        => 'rw',
    isa       => 'Str',
    default   => sub { return "(.*)"; },
    clearer   => 'clear_sample_rule',
    predicate => 'has_sample_rule',
);

=head3 maxdepth

Like find -max_depth

=cut

has 'maxdepth' => (
    is      => 'rw',
    default => 1
);

=head3 sample_glob

Alternately, instead of sample_rule use sample_glob to find files. Glob does not
differentiate between files and directories.

=cut

has 'sample_glob' => (
    is        => 'rw',
    isa       => 'Str',
    clearer   => 'clear_sample_glob',
    predicate => 'has_sample_glob',
);

=head2 find_sample_bydir

#Previous find_by_dir

Use this option when you sample names are by directory
The default is to find samples by filename

    /SAMPLE1
        SAMPLE1_r1.fastq.gz
        SAMPLE1_r2.fastq.gz
    /SAMPLE2
        SAMPLE2_r1.fastq.gz
        SAMPLE2_r2.fastq.gz

=cut

has 'find_sample_bydir' => (