diff --git a/lib/BioX/Workflow/Command/Utils/Plugin.pm b/lib/BioX/Workflow/Command/Utils/Plugin.pm
index 611cdee..ff0029d 100644
--- a/lib/BioX/Workflow/Command/Utils/Plugin.pm
+++ b/lib/BioX/Workflow/Command/Utils/Plugin.pm
@@ -59,6 +59,11 @@ after 'BUILD' => sub {
 
     $self->app_load_plugins( $self->plugins );
     $self->parse_plugin_opts( $self->plugins_opts );
+
+    ##Must reload the configs to get any options from the plugins
+    if ( $self->has_config_files ) {
+        $self->load_configs;
+    }
 };
 
 =head3 app_load_plugin
diff --git a/lib/BioX/Workflow/Command/run/Utils/Directives.pm b/lib/BioX/Workflow/Command/run/Utils/Directives.pm
index 5f60834..1fc67c4 100644
--- a/lib/BioX/Workflow/Command/run/Utils/Directives.pm
+++ b/lib/BioX/Workflow/Command/run/Utils/Directives.pm
@@ -426,6 +426,9 @@ sub create_attr {
                 if ( $k eq 'stash' ) {
                     $self->merge_stash($v);
                 }
+                elsif($self->can($k)){
+                  next;
+                }
                 elsif ( $k =~ m/_list/ ) {
                     $self->create_ITERABLE_attr( $meta, $k );
                 }
@@ -592,11 +595,12 @@ sub interpol_directive {
     my $source = shift;
     my $text   = '';
 
-    if ( exists $self->interpol_directive_cache->{$source} && $source !~ m/{\$/ ) {
+    #The $ is not always at the beginning
+    if ( exists $self->interpol_directive_cache->{$source} && $source !~ m/{/ ) {
         return $self->interpol_directive_cache->{$source};
     }
 
-    if ( $source !~ m/{\$/ ) {
+    if ( $source !~ m/{/ ) {
         $self->interpol_directive_cache->{$source} = $source;
         return $source;
     }
diff --git a/lib/BioX/Workflow/Command/run/Utils/Rules.pm b/lib/BioX/Workflow/Command/run/Utils/Rules.pm
index c13f570..b28016f 100644
--- a/lib/BioX/Workflow/Command/run/Utils/Rules.pm
+++ b/lib/BioX/Workflow/Command/run/Utils/Rules.pm
@@ -490,36 +490,6 @@ sub sanity_check_rule {
         'Rule: ' . $self->rule_name . ' passes sanity check' );
 }
 
-sub sanity_check_fail {
-    my $self = shift;
-
-    my $rule_example = <<EOF;
-global:
-    - indir: data/raw
-    - outdir: data/processed
-    - file_rule: (sample.*)$
-    - by_sample_outdir: 1
-    - find_sample_bydir: 1
-    - copy1:
-        local:
-            - indir: '{\$self->my_dir}'
-            - INPUT: '{\$self->indir}/{\$sample}.csv'
-            - HPC:
-                - mem: '40GB'
-                - walltime: '40GB'
-        process: |
-            echo 'MyDir on {\$self->my_dir}'
-            echo 'Indir on {\$self->indir}'
-            echo 'Outdir on {\$self->outdir}'
-            echo 'INPUT on {\$self->INPUT}'
-EOF
-    $self->app_log->fatal('Skipping this rule.');
-    $self->app_log->fatal(
-'Here is an example workflow. For more information please see biox-workflow.pl new --help.'
-    );
-    $self->app_log->fatal($rule_example);
-}
-
 =head3 template_process
 
 Do the actual processing of the rule->process
@@ -554,6 +524,15 @@ sub template_process {
       $self->write_rule_meta('before_meta');
 }
 
+=head3 use_iterables
+
+Check the global and local keys to see if we are using any iterables
+
+  use_chroms: 1
+  use_chunks: 1
+
+=cut
+
 sub use_iterables {
     my $self = shift;
 
@@ -937,4 +916,33 @@ sub carry_directives {
     $self->local_attr->stash( dclone( $self->p_local_attr->stash ) );
 }
 
+sub sanity_check_fail {
+    my $self = shift;
+
+    my $rule_example = <<EOF;
+global:
+    - indir: data/raw
+    - outdir: data/processed
+    - file_rule: (sample.*)$
+    - by_sample_outdir: 1
+    - find_sample_bydir: 1
+    - copy1:
+        local:
+            - indir: '{\$self->my_dir}'
+            - INPUT: '{\$self->indir}/{\$sample}.csv'
+            - HPC:
+                - mem: '40GB'
+                - walltime: '40GB'
+        process: |
+            echo 'MyDir on {\$self->my_dir}'
+            echo 'Indir on {\$self->indir}'
+            echo 'Outdir on {\$self->outdir}'
+            echo 'INPUT on {\$self->INPUT}'
+EOF
+    $self->app_log->fatal('Skipping this rule.');
+    $self->app_log->fatal(
+'Here is an example workflow. For more information please see biox-workflow.pl new --help.'
+    );
+    $self->app_log->fatal($rule_example);
+}
 1;
diff --git a/lib/BioX/Workflow/Command/run/Utils/Samples.pm b/lib/BioX/Workflow/Command/run/Utils/Samples.pm
index ab76403..5777615 100644
--- a/lib/BioX/Workflow/Command/run/Utils/Samples.pm
+++ b/lib/BioX/Workflow/Command/run/Utils/Samples.pm
@@ -152,16 +152,14 @@ sub get_samples {
     #Stupid resample
     $self->get_global_keys;
 
-    if ( $self->has_samples && !$self->resample ) {
-        my (@samples) = $self->sorted_samples;
-        $self->samples( \@samples );
-        return;
-    }
+    my $exists = $self->check_sample_exist;
+    return if $exists;
 
     #We need to evaluate the global_dirs incase the indir has a var
     #But we don't keep it around, because that would be madness
     #TODO Fix this we should process these the same way we process rule names
-    $attr       = dclone( $self->global_attr );
+    $attr = dclone( $self->global_attr );
+
     # $DB::single = 2;
     if ( $attr->indir =~ m/\{\$/ ) {
         $attr->walk_process_data( $self->global_keys );
@@ -225,6 +223,28 @@ sub get_samples {
     $self->write_sample_meta;
 }
 
+sub check_sample_exist {
+    my $self = shift;
+
+    my $exists  = 0;
+    if ( $self->has_samples && !$self->resample ) {
+        my (@samples) = $self->sorted_samples;
+        $self->samples( \@samples );
+        $self->app_log->info('Samples passed in on command line.');
+        $exists = 1;
+    }
+    elsif ( $self->global_attr->has_samples ) {
+        my (@samples) = @{$self->global_attr->samples};
+        @samples = sort(@samples);
+        $self->samples( \@samples );
+        $self->app_log->info('Samples were defined in the global key.');
+        $exists = 1;
+    }
+
+    $self->write_sample_meta if $exists;
+    return $exists;
+}
+
 =head2 match_samples
 
 Match samples based on regex written in sample_rule
diff --git a/t/lib/TestsFor/BioX/Workflow/Command/run/Test006.pm b/t/lib/TestsFor/BioX/Workflow/Command/run/Test006.pm
index 82351a3..eedfa6d 100644
--- a/t/lib/TestsFor/BioX/Workflow/Command/run/Test006.pm
+++ b/t/lib/TestsFor/BioX/Workflow/Command/run/Test006.pm
@@ -154,16 +154,6 @@ sub test_002 {
 
 }
 
-sub create_times {
-    my $now = DateTime->now( time_zone => 'local' );
-    my $strp = DateTime::Format::Strptime->new(
-        pattern   => '%a %b %e %T %Y',
-        time_zone => 'local',
-    );
-
-    return $now, $strp;
-}
-
 sub _init_rule {
     my $test = shift;
     my $rule = shift;
diff --git a/t/lib/TestsFor/BioX/Workflow/Command/run/Test007.pm b/t/lib/TestsFor/BioX/Workflow/Command/run/Test007.pm
new file mode 100644
index 0000000..9413010
--- /dev/null
+++ b/t/lib/TestsFor/BioX/Workflow/Command/run/Test007.pm
@@ -0,0 +1,114 @@
+package TestsFor::BioX::Workflow::Command::run::Test007;
+
+use Test::Class::Moose;
+use Cwd;
+use FindBin qw($Bin);
+use File::Path qw(make_path remove_tree);
+use Data::Dumper;
+use Capture::Tiny ':all';
+use BioX::Workflow::Command;
+use YAML::XS;
+use Data::Walk;
+use File::Slurp;
+use File::Spec;
+use DateTime;
+use DateTime::Format::Strptime;
+use Storable qw(dclone);
+
+extends 'TestMethod::Base';
+
+sub write_test_file {
+    my $test_dir = shift;
+
+    my $fh;
+    my $href = {
+        global => [
+            { sample_rule       => "Sample_.*" },
+            { root_dir          => 'data/raw' },
+            { indir             => '{$self->root_dir}' },
+            { outdir            => 'data/processed' },
+            { find_sample_bydir => 1 },
+            { by_sample_outdir  => 1 },
+            { chroms_list => [1,2,3,4,5]},
+            { samples => ['Sample_01']},
+        ],
+        rules => [
+            {
+                t3_rule1 => {
+                    'local' => [
+                        { root_dir => 'data/raw' },
+                        {
+                            INPUT =>
+'{$self->root_dir}/{$sample}/some_input_rule1.{$self->chunk}'
+                        },
+                        { OUTPUT => ['some_output_rule1'] },
+                        { use_chunks => 1 },
+                    ],
+                    process =>
+'R1: INDIR: {$self->indir} INPUT: {$self->INPUT} outdir: {$self->outdir} OUTPUT: {$self->OUTPUT->[0]}',
+                },
+            },
+        ]
+    };
+
+    #Write out the config
+    open( $fh, ">$test_dir/conf/test1.1.yml" )
+      or die print "Couldn't open file! $!";
+    my $yaml = Dump $href;
+    print $fh $yaml;
+    close($fh);
+
+    make_path( $test_dir . "/data/raw/Sample_01" );
+    make_path( $test_dir . "/data/raw/Sample_02" );
+    write_file( $test_dir . "/data/raw/Sample_01/" . "some_input_rule1" );
+    write_file( $test_dir . "/data/raw/Sample_02/" . "some_input_rule1" );
+}
+
+sub construct_tests {
+    my $test_methods = TestMethod::Base->new();
+    my $test_dir     = $test_methods->make_test_dir();
+    write_test_file($test_dir);
+
+    my $t     = "$test_dir/conf/test1.1.yml";
+    my $test  = $test_methods->make_test_env($t);
+    my $rules = $test->workflow_data->{rules};
+
+    return ( $test, $test_dir, $rules );
+}
+
+sub test_001 {
+    my ( $test, $test_dir, $rules ) = construct_tests;
+
+    $test->check_sample_exist;
+    is_deeply($test->samples, ['Sample_01']);
+    is_deeply($test->global_attr->chroms_list, [1,2,3,4,5]);
+
+    # $test->stdout(1);
+    $test->set_rule_names;
+    $test->filter_rule_keys;
+
+    foreach my $rule ( @{$rules} ) {
+        _init_rule( $test, $rule );
+    }
+
+    $test->post_process_rules;
+    is_deeply($test->samples, ['Sample_01']);
+
+    diag Dumper ($test->global_attr->chroms_list);
+    diag Dumper ($test->global_attr->samples);
+    diag Dumper($test->global_attr->has_samples);
+
+
+    ok(1);
+}
+
+
+sub _init_rule {
+    my $test = shift;
+    my $rule = shift;
+
+    $test->local_rule($rule);
+    $test->process_rule;
+    $test->p_rule_name( $test->rule_name );
+    $test->p_local_attr( dclone( $test->local_attr ) );
+}
diff --git a/t/test_class_tests.t b/t/test_class_tests.t
index d807341..76ba9dd 100644
--- a/t/test_class_tests.t
+++ b/t/test_class_tests.t
@@ -13,5 +13,6 @@ Test::Class::Moose::Runner->new(
         'TestsFor::BioX::Workflow::Command::run::Test004',
         'TestsFor::BioX::Workflow::Command::run::Test005',
         'TestsFor::BioX::Workflow::Command::run::Test006',
+        'TestsFor::BioX::Workflow::Command::run::Test007',
     ],
 )->runtests;