Merge branch 'master' into develop

Author: jerowe

Changes

@@ -2,6 +2,12 @@ Revision history for BioX-Workflow-Command
 
 {{$NEXT}}
 
+2.0.8  2017-05-04 14:30:02 +04
+	- Cleaned up logging to create a table - no more wall of text!
+	- Fixed HPC meta to correctly overwrite global when global/local are arrayref of keys
+	- Follow symbolic links when looking for Samples
+	- Throw an error when making a directory fails
+
 2.0.7  2017-05-01 12:32:58 +04
 	- Added in chunking functionality
 

META.json

@@ -110,7 +110,7 @@
          "web" : "https://github.com/jerowe/BioX-Workflow-Command"
       }
    },
-   "version" : "2.0.7",
+   "version" : "2.0.8",
    "x_serialization_backend" : "Cpanel::JSON::XS version 3.0225"
 }
 

lib/BioX/Workflow/Command.pm

@@ -1,7 +1,7 @@
 package BioX::Workflow::Command;
 
 use v5.10;
-our $VERSION = '2.0.7';
+our $VERSION = '2.0.8';
 
 use MooseX::App qw(Color);
 use MooseX::Types::Path::Tiny qw/Path/;

lib/BioX/Workflow/Command/run/Utils/Directives.pm

@@ -264,6 +264,13 @@ has 'HPC' => (
 ##This is useful for features where we want to do things like
 ##split a file into parts
 ##count by kmers, etc
+=head2 Iterables
+
+Lists to iterate by
+
+Chunks and chroms are included by default
+
+=cut
 
 has 'chunks' => (
     is      => 'rw',
@@ -283,6 +290,15 @@ has 'use_chunks' => (
     }
 );
 
+
+has 'chroms' => (
+is => 'rw',
+isa => 'ArrayRef',
+default => sub {
+  return [1 .. 22, 'X', 'Y', 'MT'];
+},
+)
+
 =head2 stash
 
 This isn't ever used in the code. Its just there incase you want to persist objects across rules

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

@@ -6,6 +6,7 @@ use Data::Merger qw(merger);
 use Data::Walk;
 use Data::Dumper;
 use File::Path qw(make_path remove_tree);
+use Try::Tiny;
 
 with 'BioX::Workflow::Command::Utils::Files::TrackChanges';
 use BioX::Workflow::Command::Utils::Traits qw(ArrayRefOfStrs);
@@ -655,8 +656,16 @@ sub walk_attr {
 
     $attr->walk_process_data( $self->rule_keys );
 
-    if ( $attr->create_outdir ) {
-        make_path( $attr->outdir );
+    if ( $attr->create_outdir && !$attr->outdir->is_dir ) {
+
+        try {
+            $attr->outdir->mkpath;
+        }
+        catch {
+            $self->app_log->fatal( "We were not able to make the directory.\n\t"
+                  . $attr->outdir
+                  . "\n\tError: $!" );
+        };
     }
 
     return $attr;

t/lib/TestsFor/BioX/Workflow/Command/run/Test004.pm

@@ -152,6 +152,7 @@ sub test_001 {
     my $expect_log = <<EOF;
 ; \\
 biox file_log \\
+\t--exit_code `echo \$\?`  \\
 \t--file $test_dir/data/raw/Sample_02/some_input_rule1 \\
 \t--file $test_dir/some_output_rule1\n
 EOF