Merge branch 'master' into develop

Author: jerowe

META.json

@@ -4,7 +4,7 @@
       "Jillian Rowe <[email protected]>"
    ],
    "dynamic_config" : 0,
-   "generated_by" : "Dist::Milla version v1.0.17, Dist::Zilla version 6.008, CPAN::Meta::Converter version 2.150001",
+   "generated_by" : "Dist::Milla version v1.0.17, Dist::Zilla version 6.009, CPAN::Meta::Converter version 2.150001",
    "license" : [
       "perl_5"
    ],
@@ -39,9 +39,9 @@
          "requires" : {
             "Algorithm::Dependency::Ordered" : "0",
             "Algorithm::Dependency::Source::HoA" : "0",
+            "BioX::Workflow::Command::run::Utils::Rules" : "0",
             "Config::Any" : "0",
             "Cwd" : "0",
-            "DBM::Deep" : "0",
             "Data::Dumper" : "0",
             "Data::Merger" : "0",
             "Data::Walk" : "0",
@@ -61,7 +61,7 @@
             "Memoize" : "0",
             "Moose" : "0",
             "Moose::Role" : "0",
-            "Moose::Util::TypeConstraints" : "0",
+            "Moose::Util" : "0",
             "MooseX::App" : "0",
             "MooseX::App::Command" : "0",
             "MooseX::App::Role" : "0",
@@ -72,10 +72,10 @@
             "Number::Bytes::Human" : "0",
             "Path::Tiny" : "0",
             "Safe" : "0",
-            "Scalar::Util" : "0",
             "Storable" : "0",
             "String::Approx" : "0",
             "Text::ASCIITable" : "0",
+            "Text::CSV::Slurp" : "0",
             "Text::Template" : "0",
             "Time::localtime" : "0",
             "Try::Tiny" : "0",
@@ -91,7 +91,9 @@
             "Capture::Tiny" : "0",
             "File::Slurp" : "0",
             "File::Spec::Functions" : "0",
+            "File::Temp" : "0",
             "FindBin" : "0",
+            "JSON" : "0",
             "Test::Class::Moose" : "0",
             "Test::Class::Moose::Load" : "0",
             "Test::Class::Moose::Runner" : "0",
@@ -114,6 +116,6 @@
       }
    },
    "version" : "2.0.10",
-   "x_serialization_backend" : "Cpanel::JSON::XS version 3.0225"
+   "x_serialization_backend" : "Cpanel::JSON::XS version 3.0233"
 }
 

README.md

@@ -28,18 +28,10 @@ Full documentation is available at gitbooks. [Documentation ](https://metacpan.o
 
 ## Run a Workflow with make like utilities
 
-Using the option --use\_timestamps will select only rules that have INPUT/OUTPUT that does not exist or has been modified since the last log.
-
-    biox run --workflow workflow.yml --use_timestamps
-
 Using the option --auto\_deps will create #HPC deps based on your INPUT/OUTPUTs - use this with caution. It will only work correctly if INPUT/OUTPUT is complete and accurate.
 
     biox run --workflow workflow.yml --auto_deps
 
-Option --make enables both --use\_timestamps and --auto\_deps
-
-    biox run --workflow workflow.yml --make
-
 ## Create a new workflow
 
 This creates a new workflow with rules rule1, rule2, rule3, with a few variables to help get you started.

lib/BioX/Workflow/Command.pm

@@ -84,21 +84,18 @@ Full documentation is available at gitbooks. L<Documentation | https://biosails.
 
 =head2 Run a Workflow with make like utilities
 
-Using the option --use_timestamps will select only rules that have INPUT/OUTPUT that does not exist or has been modified since the last log.
 
-  biox run --workflow workflow.yml --use_timestamps
-
-Using the option --auto_deps will create #HPC deps based on your INPUT/OUTPUTs - use this with caution. It will only work correctly if INPUT/OUTPUT is complete and accurate.
+Using the option --auto_deps will create #HPC deps based on your INPUT/OUTPUTs -
+use this with caution. It will only work correctly if INPUT/OUTPUT is complete
+and accurate.
 
   biox run --workflow workflow.yml --auto_deps
 
-Option --make enables both --use_timestamps and --auto_deps
-
-  biox run --workflow workflow.yml --make
 
 =head2 Create a new workflow
 
-This creates a new workflow with rules rule1, rule2, rule3, with a few variables to help get you started.
+This creates a new workflow with rules rule1, rule2, rule3, with a few variables
+to help get you started.
 
   biox new -w workflow.yml --rules rule1,rule2,rule3
 
@@ -110,7 +107,8 @@ Add new rules to an existing workflow.
 
 =head2 Check the status of files in your workflow
 
-You must have defined INPUT/OUTPUTs to make use of this rule. If you do, biox will output a table with information about your files.
+You must have defined INPUT/OUTPUTs to make use of this rule. If you do, biox
+will output a table with information about your files.
 
   biox stats -w workflow.yml
 

lib/BioX/Workflow/Command/stats.pm

@@ -29,9 +29,7 @@ command_short_description 'Get the status of INPUT/OUTPUT for your workflow';
 command_long_description
   'If you are unsure on where you are in your workflow, run this step. '
   . 'It will give you a breakdown of rules with associated files, '
-  . 'and whether or not they have been created or modified. '
-  . 'Automatically select rules with unprocessed or changed files by using '
-  . '--use_timestamps in your next run.';
+  . 'and whether or not they have been created or modified. ';
 
 has 'app_log_file' => (
     is      => 'rw',