Merge branch 'develop'

Author: jerowe

lib/BioX/Workflow/Command/run/Rules/Rules.pm

@@ -695,7 +695,7 @@ sub walk_indir_outdir {
 
     my $text = $attr->interpol_directive( $attr->outdir );
 
-    $DB::single = 2;
+    # $DB::single = 2;
     $self->walk_indir_outdir_sample( $attr, $text );
 }
 
@@ -846,7 +846,7 @@ sub check_indir_outdir {
     my $self = shift;
     my $attr = shift;
 
-    $DB::single = 2;
+    # $DB::single = 2;
     return unless $attr->by_sample_outdir;
     return unless $self->has_sample;
     return if $attr->override_process;
@@ -893,7 +893,7 @@ Outdir should be global_attr->outdir/rule_name
 sub carry_directives {
     my $self = shift;
 
-    $DB::single = 2;
+    # $DB::single = 2;
     $self->local_attr->outdir(
         $self->global_attr->outdir . '/' . $self->rule_name );
 

lib/BioX/Workflow/Command/run/Utils/Files/ResolveDeps.pm

@@ -44,6 +44,9 @@ sub add_graph {
     my $self = shift;
     my $cond = shift;
 
+    return unless $self->files;
+    return unless $self->has_files;
+
     for my $file ( $self->all_files ) {
         if ( !exists $self->rule_deps->{ $self->rule_name }->{$cond}->{$file} )
         {

lib/BioX/Workflow/Command/run/Utils/Files/TrackChanges.pm

@@ -17,17 +17,6 @@ Files just for this rule
 ##TODO Make this a hash?
 =cut
 
-# has 'files' => (
-#     traits  => ['Hash'],
-#     is      => 'rw',
-#     isa     => 'HashRef',
-#     default => sub { {} },
-#     handles => {
-#         files_pairs => 'kv',
-#         clear_files => 'clear',
-#     },
-# );
-
 has 'files' => (
     traits  => ['Array'],
     is      => 'rw',
@@ -87,7 +76,9 @@ sub walk_INPUT {
     return unless $ref_name;
     return unless $ref_name eq 'Path::Tiny';
 
-    $self->push_files( $ref->absolute );
+    my $file = $ref->absolute;
+    $file = "$file";
+    $self->push_files( $file );
 }
 
 1;

lib/BioX/Workflow/Command/stats.pm

@@ -47,28 +47,25 @@ has 'app_log_file' => (
         return $log_file;
     }
 );
-
-has '+app_log' => (
+has 'app_log' => (
+    is      => 'rw',
     default => sub {
-        my $self         = shift;
-        my $app_log_file = $self->app_log_file;
-        my $log_conf     = <<EOF;
-  log4perl.category = DEBUG, LOGFILE
-  log4perl.appender.LOGFILE=Log::Log4perl::Appender::File
-  log4perl.appender.LOGFILE.filename=$app_log_file
-EOF
-
-        $log_conf .= <<'EOF';
-  log4perl.appender.LOGFILE.mode=append
-  log4perl.appender.LOGFILE.layout=PatternLayout
-  log4perl.appender.LOGFILE.layout.ConversionPattern=[%d] %m %n
-EOF
-
-        Log::Log4perl->init( \$log_conf );
+        my $self = shift;
+        Log::Log4perl->init( \ <<'EOT');
+  log4perl.category = FATAL, Screen
+  log4perl.appender.Screen = \
+      Log::Log4perl::Appender::ScreenColoredLevels
+  log4perl.appender.Screen.layout = \
+      Log::Log4perl::Layout::PatternLayout
+  log4perl.appender.Screen.layout.ConversionPattern = \
+      [%d] %m %n
+EOT
         return get_logger();
     },
+    lazy => 1,
 );
 
+
 has 'table_log' => (
     is      => 'rw',
     default => sub {
@@ -120,6 +117,11 @@ around 'pre_FILES' => sub {
 
     $self->$orig( $attr, $cond );
 
+    return unless $self->has_files;
+    return unless $self->files;
+
+    $DB::single=2;
+
     for my $file ( $self->all_files ) {
         $self->preprocess_row( $file, $cond );
     }