Merge branch 'develop'

Author: jerowe

lib/BioX/Workflow/Command.pm

@@ -11,6 +11,15 @@ use File::Path qw(make_path);
 
 app_strict 0;
 
+with 'BioX::Workflow::Command::Utils::Log';
+with 'BioX::Workflow::Command::Utils::Plugin';
+with 'HPC::Runner::Command::Utils::ManyConfigs';
+
+option 'config_base' => (
+    is      => 'rw',
+    default => '.bioxworkflow',
+);
+
 option 'cache_dir' => (
     is      => 'rw',
     isa     => Path,
@@ -21,19 +30,19 @@ option 'cache_dir' => (
     documentation =>
       'BioX-Workflow will cache some information during your runs. '
       . 'Delete with caution! '
-      . '[Default: '.getcwd().'/biox-cache. ]'
+      . '[Default: '
+      . getcwd()
+      . '/biox-cache. ]'
 );
 
-sub BUILD {
-  my $self = shift;
-}
+sub BUILD {}
 
 before 'BUILD' => sub {
     my $self = shift;
 
     make_path( $self->cache_dir );
-    make_path(File::Spec->catdir($self->cache_dir, 'logs'));
-    make_path(File::Spec->catdir($self->cache_dir, 'workflows'));
+    make_path( File::Spec->catdir( $self->cache_dir, 'logs' ) );
+    make_path( File::Spec->catdir( $self->cache_dir, 'workflows' ) );
 };
 
 no Moose;

lib/BioX/Workflow/Command/Utils/Plugin.pm

@@ -3,6 +3,7 @@ package BioX::Workflow::Command::Utils::Plugin;
 use MooseX::App::Role;
 
 #TODO make this into a general Plugin Loader
+with 'BioX::Workflow::Command::Utils::Log';
 
 use Cwd qw(getcwd);
 use Try::Tiny;
@@ -49,25 +50,16 @@ option 'plugins_opts' => (
 
 =cut
 
-sub BUILD {}
+sub BUILD { }
 
 after 'BUILD' => sub {
-  my $self = shift;
-
-  return unless $self->plugins;
-
-  $self->app_load_plugins( $self->plugins );
-  $self->parse_plugin_opts( $self->plugins_opts );
-};
-
-sub gen_load_plugins {
     my $self = shift;
 
     return unless $self->plugins;
 
     $self->app_load_plugins( $self->plugins );
     $self->parse_plugin_opts( $self->plugins_opts );
-}
+};
 
 =head3 app_load_plugin
 
@@ -85,7 +77,8 @@ sub app_load_plugins {
         }
         catch {
             $self->app_log->warn("Could not load plugin $plugin!\n$_");
-        }
+        };
+        $self->app_log->info( 'Loaded plugin ' . $plugin );
     }
 
 }

lib/BioX/Workflow/Command/run.pm

@@ -15,9 +15,10 @@ with 'BioX::Workflow::Command::run::Utils::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::Log';
 with 'BioX::Workflow::Command::Utils::Files';
-with 'BioX::Workflow::Command::Utils::Plugin';
+
+# with 'BioX::Workflow::Command::Utils::Plugin';
+# with 'BioX::Workflow::Command::Utils::Log';
 
 command_short_description 'Run your workflow';
 command_long_description
@@ -29,7 +30,6 @@ This is the main class of the `biox-workflow.pl run` command.
 
 =cut
 
-
 =head2 Attributes
 
 =cut
@@ -41,15 +41,14 @@ This is the main class of the `biox-workflow.pl run` command.
 sub execute {
     my $self = shift;
 
-    $self->app_log->info('Printing out file info for '.$self->workflow);
+    $self->app_log->info( 'Printing out file info for ' . $self->workflow );
     $self->print_opts;
-    if(! $self->load_yaml_workflow){
-      $self->app_log->warn('Exiting now.');
-      return;
+    if ( !$self->load_yaml_workflow ) {
+        $self->app_log->warn('Exiting now.');
+        return;
     }
 
-
-        copy($self->workflow, $self->cached_workflow );
+    copy( $self->workflow, $self->cached_workflow );
     $self->apply_global_attributes;
     $self->get_global_keys;
     $self->get_samples;
@@ -60,6 +59,7 @@ sub execute {
 }
 
 no Moose;
+
 __PACKAGE__->meta->make_immutable;
 
 1;

lib/BioX/Workflow/Command/stats.pm

@@ -140,8 +140,7 @@ sub gen_row {
     my $sample       = shift;
     my $sample_files = shift;
 
-    my @uniq = uniq(@{$sample_files});
-    foreach my $file (@uniq) {
+    foreach my $file (@{$sample_files}) {
 
         my @trow = ();
 
@@ -195,6 +194,7 @@ sub iter_file_samples {
         else {
             push( @sample_files, $new_file );
         }
+        @sample_files = uniq(@sample_files);
         $self->gen_row( $file, $cond, $sample, \@sample_files );
     }
 }