Merge f615262 into 1e109a6

Clinical-Genomics · Dec 14, 2020 · b49e035 · b49e035
2 parents 1e109a6 + f615262
commit b49e035
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diff --git a/.perlcriticrc b/.perlcriticrc
@@ -9,6 +9,8 @@ lines = 100
 functions = :builtins
 exclude_functions = print say
 
+[-Perl::Critic::Policy::Modules::RequireVersionVar]
+
 ## Perltidy has already been run with a diffrent slightlty modified rules
 [-CodeLayout::RequireTidyCode]
 
diff --git a/documentation/API/Tests.md b/documentation/API/Tests.md
@@ -53,8 +53,7 @@ use MIP::Program::Conda qw{conda_install};
 #### Diagnose string
 Change:
 ```Perl
-diag(   q{Test SUB_ROUTINE from MODULE_NAME.pm v}
-      . $MIP::PATH::TO::MODULE::VERSION
+diag(   q{Test SUB_ROUTINE from MODULE_NAME.pm}
       . $COMMA
       . $SPACE . q{Perl}
       . $SPACE
@@ -64,8 +63,7 @@ diag(   q{Test SUB_ROUTINE from MODULE_NAME.pm v}
 ```
 To:
 ```Perl
-diag(   q{Test conda_install from Conda.pm v}
-      . $MIP::Program::Conda::VERSION
+diag(   q{Test conda_install from Conda.pm}
       . $COMMA
       . $SPACE . q{Perl}
       . $SPACE

diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -27,9 +27,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.34;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       add_gender

diff --git a/lib/MIP/Analysis.pm b/lib/MIP/Analysis.pm
@@ -28,9 +28,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.28;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       broadcast_parameters

diff --git a/lib/MIP/Check/Reference.pm b/lib/MIP/Check/Reference.pm
@@ -22,8 +22,7 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.19;
+
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{

diff --git a/lib/MIP/Cli/Mip/Analyse.pm b/lib/MIP/Cli/Mip/Analyse.pm
@@ -21,8 +21,6 @@ use Moose::Util::TypeConstraints;
 use MIP::Cli::Utils qw{ run };
 
 # Set the version for version checking
-our $VERSION = 1.16;
-
 extends(qw{ MIP::Cli::Mip });
 
 command_short_description(q{MIP analyse command});

diff --git a/lib/MIP/Cli/Mip/Analyse/Dragen_rd_dna.pm b/lib/MIP/Cli/Mip/Analyse/Dragen_rd_dna.pm
@@ -17,8 +17,6 @@ use Moose::Util::TypeConstraints;
 ## MIPs lib
 use MIP::Main::Analyse qw{ mip_analyse };
 
-our $VERSION = 1.20;
-
 extends(qw{ MIP::Cli::Mip::Analyse });
 
 command_short_description(q{Dragen rare disease DNA analysis});

diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
@@ -16,8 +16,6 @@ use Moose::Util::TypeConstraints;
 ## MIPs lib
 use MIP::Main::Analyse qw{ mip_analyse };
 
-our $VERSION = 1.64;
-
 extends(qw{ MIP::Cli::Mip::Analyse });
 
 command_short_description(q{Rare disease DNA analysis});

diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna_panel.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna_panel.pm
@@ -16,8 +16,6 @@ use Moose::Util::TypeConstraints;
 ## MIPs lib
 use MIP::Main::Analyse qw{ mip_analyse };
 
-our $VERSION = 1.13;
-
 extends(qw{ MIP::Cli::Mip::Analyse });
 
 command_short_description(q{Rare disease DNA analysis of panels});

diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna_vcf_rerun.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna_vcf_rerun.pm
@@ -16,8 +16,6 @@ use Moose::Util::TypeConstraints;
 ## MIPs lib
 use MIP::Main::Analyse qw{ mip_analyse };
 
-our $VERSION = 1.34;
-
 extends(qw{ MIP::Cli::Mip::Analyse });
 
 command_short_description(q{Rare disease DNA vcf rerun analysis});

diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_rna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_rna.pm
@@ -16,8 +16,6 @@ use Moose::Util::TypeConstraints;
 ## MIPs lib
 use MIP::Main::Analyse qw{ mip_analyse };
 
-our $VERSION = 1.40;
-
 extends(qw{ MIP::Cli::Mip::Analyse });
 
 command_short_description(q{Rare disease RNA analysis});

diff --git a/lib/MIP/Cli/Mip/Download.pm b/lib/MIP/Cli/Mip/Download.pm
@@ -19,8 +19,6 @@ use MooseX::Types::Moose qw{ ArrayRef Bool HashRef Int Str };
 use MIP::Definition qw{ get_parameter_from_definition_files };
 use MIP::Main::Download qw{ mip_download };
 
-our $VERSION = 1.05;
-
 extends(qw{ MIP::Cli::Mip });
 
 command_short_description(q{Generate bash or sbatch for download of references});

diff --git a/lib/MIP/Cli/Mip/Install.pm b/lib/MIP/Cli/Mip/Install.pm
@@ -22,8 +22,6 @@ use MIP::Definition qw{ get_parameter_from_definition_files };
 use MIP::Get::Parameter qw{ get_install_parameter_attribute };
 use MIP::Main::Install qw{ mip_install };
 
-our $VERSION = 1.26;
-
 extends(qw{ MIP::Cli::Mip });
 
 command_short_description(q{MIP install command});

diff --git a/lib/MIP/Cli/Mip/Qccollect.pm b/lib/MIP/Cli/Mip/Qccollect.pm
@@ -19,8 +19,6 @@ use MooseX::Types::Moose qw{ ArrayRef Bool HashRef Int Str };
 ## MIPs lib/
 use MIP::Constants qw{ $NEWLINE };
 
-our $VERSION = 1.02;
-
 command_short_description(q{MIP qccollect command});
 
 command_long_description(q{Entry point for collecting MIP QC metrics});

diff --git a/lib/MIP/Cli/Mip/Vcfparser.pm b/lib/MIP/Cli/Mip/Vcfparser.pm
@@ -26,8 +26,6 @@ use MIP::Constants qw{ %ANALYSIS $COLON $DASH $NEWLINE };
 use MIP::Log::MIP_log4perl qw{ initiate_logger };
 use MIP::Main::Vcfparser qw{ mip_vcfparser };
 
-our $VERSION = 1.02;
-
 command_short_description(q{MIP vcfparser command});
 
 command_long_description(

diff --git a/lib/MIP/Cli/Utils.pm b/lib/MIP/Cli/Utils.pm
@@ -17,9 +17,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.02;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ run };
 }

diff --git a/lib/MIP/Cluster.pm b/lib/MIP/Cluster.pm
@@ -24,9 +24,6 @@ BEGIN {
     use base qw{ Exporter };
     require Exporter;
 
-    # Set the version for version checking
-    our $VERSION = 1.07;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       get_core_number

diff --git a/lib/MIP/Config.pm b/lib/MIP/Config.pm
@@ -22,9 +22,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.07;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ check_cmd_config_vs_definition_file
       get_install_containers

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
@@ -19,9 +19,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.27;
-
     # Functions and variables which can be optionally exported
 
     our @EXPORT_OK = qw{

diff --git a/lib/MIP/Contigs.pm b/lib/MIP/Contigs.pm
@@ -24,9 +24,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.11;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       check_select_file_contigs

diff --git a/lib/MIP/Definition.pm b/lib/MIP/Definition.pm
@@ -24,9 +24,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.06;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ check_definition_file
       get_dependency_tree_from_definition_file

diff --git a/lib/MIP/Dependency_tree.pm b/lib/MIP/Dependency_tree.pm
@@ -23,9 +23,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.01;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ get_dependency_tree
       get_dependency_tree_chain

diff --git a/lib/MIP/Download.pm b/lib/MIP/Download.pm
@@ -21,9 +21,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.00;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ check_user_reference get_download_reference_attributes };
 }

diff --git a/lib/MIP/Environment/Child_process.pm b/lib/MIP/Environment/Child_process.pm
@@ -19,9 +19,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.01;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ child_process };
 }

diff --git a/lib/MIP/Environment/Cluster.pm b/lib/MIP/Environment/Cluster.pm
@@ -22,9 +22,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.00;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ check_max_core_number
       check_recipe_memory_allocation

diff --git a/lib/MIP/Environment/Container.pm b/lib/MIP/Environment/Container.pm
@@ -22,9 +22,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.05;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       build_container_cmd

diff --git a/lib/MIP/Environment/Executable.pm b/lib/MIP/Environment/Executable.pm
@@ -21,9 +21,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.14;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       build_binary_version_cmd

diff --git a/lib/MIP/Environment/Manager.pm b/lib/MIP/Environment/Manager.pm
@@ -21,9 +21,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.01;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ get_env_method_cmds write_source_environment_command };
 }

diff --git a/lib/MIP/Environment/Path.pm b/lib/MIP/Environment/Path.pm
@@ -26,9 +26,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.05;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       get_conda_path

diff --git a/lib/MIP/Environment/User.pm b/lib/MIP/Environment/User.pm
@@ -21,9 +21,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.01;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ check_email_address };
 }

diff --git a/lib/MIP/Fastq.pm b/lib/MIP/Fastq.pm
@@ -24,9 +24,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.05;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       casava_header_features

diff --git a/lib/MIP/File/Decompression.pm b/lib/MIP/File/Decompression.pm
@@ -21,9 +21,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.05;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ decompress_files };
 }

diff --git a/lib/MIP/File/Format/Dragen.pm b/lib/MIP/File/Format/Dragen.pm
@@ -24,9 +24,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.00;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ create_dragen_fastq_list_sample_id };
 }

diff --git a/lib/MIP/File/Format/Feature_file.pm b/lib/MIP/File/Format/Feature_file.pm
@@ -23,9 +23,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.02;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK =
       qw{ parse_feature_file_data parse_feature_file_header read_feature_file set_vcf_header_info tree_annotations };

diff --git a/lib/MIP/File/Format/Mip.pm b/lib/MIP/File/Format/Mip.pm
@@ -18,9 +18,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.03;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{  };
 }

diff --git a/lib/MIP/File/Format/Pli.pm b/lib/MIP/File/Format/Pli.pm
@@ -22,9 +22,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.00;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ load_pli_file };
 }

diff --git a/lib/MIP/File/Format/Star_fusion.pm b/lib/MIP/File/Format/Star_fusion.pm
@@ -23,9 +23,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.02;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ create_star_fusion_sample_file };
 }

diff --git a/lib/MIP/File/Format/Vcf.pm b/lib/MIP/File/Format/Vcf.pm
@@ -22,9 +22,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.02;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       check_vcf_variant_line

diff --git a/lib/MIP/File/Format/Vep.pm b/lib/MIP/File/Format/Vep.pm
@@ -24,9 +24,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.00;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ create_vep_synonyms_file };
 }

diff --git a/lib/MIP/File/Path.pm b/lib/MIP/File/Path.pm
@@ -24,9 +24,6 @@ BEGIN {
     require Exporter;
     use base qw{ Exporter };
 
-    # Set the version for version checking
-    our $VERSION = 1.06;
-
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
       check_allowed_temp_directory