Merge 151dc98 into b849964

Clinical-Genomics · Nov 19, 2019 · 153a173 · 153a173
2 parents b849964 + 151dc98
commit 153a173
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Showing 3 changed files with 75 additions and 150 deletions.
diff --git a/lib/MIP/Program/Qc/Multiqc.pm → lib/MIP/Program/Multiqc.pm b/lib/MIP/Program/Qc/Multiqc.pm → lib/MIP/Program/Multiqc.pm
@@ -1,19 +1,22 @@
-package MIP::Program::Qc::Multiqc;
+package MIP::Program::Multiqc;
 
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
 use strict;
+use utf8;
 use warnings;
 use warnings qw{ FATAL utf8 };
-use utf8;
-use open qw{ :encoding(UTF-8) :std };
-use charnames qw{ :full :short };
-use Carp;
-use English qw{ -no_match_vars };
-use Params::Check qw{ check allow last_error };
 
 ## CPANM
+use autodie qw{ :all };
 use Readonly;
 
 ## MIPs lib/
+use MIP::Constants qw{ $SPACE };
 use MIP::Unix::Standard_streams qw{ unix_standard_streams };
 use MIP::Unix::Write_to_file qw{ unix_write_to_file };
 
@@ -22,100 +25,91 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.00;
+    our $VERSION = 1.01;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ multiqc };
 }
 
-## Constants
-Readonly my $SPACE => q{ };
-
 sub multiqc {
 
 ## Function  : Perl wrapper for writing multiqc recipe to already open $filehandle or return commands array. Based on multiqc 0.8.dev0.
-## Returns   : "@commands"
-## Arguments : $indir_path             => Indir path
+## Returns   : @commands
+## Arguments : $filehandle             => Filehandle to write to
+##           : $force                  => Force overwrite of output files
+##           : $indir_path             => Indir path
 ##           : $outdir_path            => Outdir path
 ##           : $stderrfile_path        => Stderrfile path
-##           : $stdoutfile_path        => Stdoutfile path
-##           : $filehandle             => Filehandle to write to
 ##           : $stderrfile_path_append => Append stderr info to file
-##           : $force                  => Force overwrite of output files
+##           : $stdoutfile_path        => Stdoutfile path
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
+    my $filehandle;
     my $indir_path;
     my $outdir_path;
-    my $stdoutfile_path;
     my $stderrfile_path;
     my $stderrfile_path_append;
-    my $filehandle;
+    my $stdoutfile_path;
 
     ## Default(s)
     my $force;
 
     my $tmpl = {
+        filehandle => { store => \$filehandle, },
+        force      => {
+            allow       => [ 0, 1 ],
+            default     => 0,
+            store       => \$force,
+            strict_type => 1,
+        },
         indir_path => {
-            required    => 1,
             defined     => 1,
+            required    => 1,
+            store       => \$indir_path,
             strict_type => 1,
-            store       => \$indir_path
         },
-        outdir_path     => { strict_type => 1, store => \$outdir_path },
-        stderrfile_path => { strict_type => 1, store => \$stderrfile_path },
-        stdoutfile_path => { strict_type => 1, store => \$stdoutfile_path },
-        filehandle => { store => \$filehandle },
+        outdir_path     => { store => \$outdir_path,     strict_type => 1, },
+        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
         stderrfile_path_append =>
-          { strict_type => 1, store => \$stderrfile_path_append },
-        force => {
-            default     => 0,
-            allow       => [ 0, 1 ],
-            strict_type => 1,
-            store       => \$force
-        },
+          { store => \$stderrfile_path_append, strict_type => 1, },
+        stdoutfile_path => { store => \$stdoutfile_path, strict_type => 1, },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    # Stores commands depending on input parameters
-    my @commands = q{multiqc};
+    my @commands = qw{ multiqc };
 
-    ## Options
     if ($force) {
 
         push @commands, q{--force};
     }
 
-    ## Outdir
     if ($outdir_path) {
 
         push @commands, q{--outdir} . $SPACE . $outdir_path;
     }
 
-    ## Indir
     push @commands, $indir_path;
 
     push @commands,
       unix_standard_streams(
         {
-            stdoutfile_path        => $stdoutfile_path,
             stderrfile_path        => $stderrfile_path,
             stderrfile_path_append => $stderrfile_path_append,
+            stdoutfile_path        => $stdoutfile_path,
         }
       );
 
     unix_write_to_file(
         {
             commands_ref => \@commands,
-            separator    => $SPACE,
             filehandle   => $filehandle,
+            separator    => $SPACE,
         }
     );
-
     return @commands;
-
 }
 
 1;
diff --git a/lib/MIP/Recipes/Analysis/Multiqc.pm b/lib/MIP/Recipes/Analysis/Multiqc.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.11;
+    our $VERSION = 1.12;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_multiqc };
@@ -127,7 +127,7 @@ sub analysis_multiqc {
     use MIP::Get::Parameter qw{ get_recipe_attributes get_recipe_resources };
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
-    use MIP::Program::Qc::Multiqc qw{ multiqc };
+    use MIP::Program::Multiqc qw{ multiqc };
     use MIP::Script::Setup_script qw{ setup_script };
     use MIP::Sample_info qw{ set_recipe_metafile_in_sample_info };
 

diff --git a/t/multiqc.t b/t/multiqc.t
@@ -1,93 +1,57 @@
 #!/usr/bin/env perl
 
-use Modern::Perl qw{ 2018 };
-use warnings qw{ FATAL utf8 };
-use autodie;
 use 5.026;
-use utf8;
-use open qw{ :encoding(UTF-8) :std };
-use charnames qw{ :full :short };
 use Carp;
+use charnames qw{ :full :short };
 use English qw{ -no_match_vars };
-use Params::Check qw{ check allow last_error };
-
-use FindBin qw{ $Bin };
-use File::Basename qw{ dirname basename };
+use File::Basename qw{ dirname };
 use File::Spec::Functions qw{ catdir catfile };
-use Getopt::Long;
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
 use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw{ :all };
+use Modern::Perl qw{ 2018 };
 use Readonly;
 
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
-use MIP::Script::Utils qw{ help };
-
-our $USAGE = build_usage( {} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Commands qw{ test_function };
+use MIP::Test::Fixtures qw{ test_standard_cli };
 
 my $VERBOSE = 1;
-our $VERSION = 1.0.0;
-
-## Constants
-Readonly my $SPACE   => q{ };
-Readonly my $NEWLINE => qq{\n};
-Readonly my $COMMA   => q{,};
-
-### User Options
-GetOptions(
-
-    # Display help text
-    q{h|help} => sub {
-        done_testing();
-        say {*STDOUT} $USAGE;
-        exit;
-    },
+our $VERSION = 1.01;
 
-    # Display version number
-    q{v|version} => sub {
-        done_testing();
-        say {*STDOUT} $NEWLINE . basename($PROGRAM_NAME) . $SPACE . $VERSION . $NEWLINE;
-        exit;
-    },
-    q{vb|verbose} => $VERBOSE,
-  )
-  or (
-    done_testing(),
-    help(
-        {
-            USAGE     => $USAGE,
-            exit_code => 1,
-        }
-    )
-  );
+$VERBOSE = test_standard_cli(
+    {
+        verbose => $VERBOSE,
+        version => $VERSION,
+    }
+);
 
 BEGIN {
 
+    use MIP::Test::Fixtures qw{ test_import };
+
 ### Check all internal dependency modules and imports
 ## Modules with import
-    my %perl_module;
-
-    $perl_module{q{MIP::Script::Utils}} = [qw{ help }];
-
-  PERL_MODULE:
-    while ( my ( $module, $module_import ) = each %perl_module ) {
-        use_ok( $module, @{$module_import} )
-          or BAIL_OUT q{Cannot load} . $SPACE . $module;
-    }
-
-## Modules
-    my @modules = (q{MIP::Program::Qc::Multiqc});
+    my %perl_module = (
+        q{MIP::Program::Multiqc} => [qw{ multiqc }],
+        q{MIP::Test::Fixtures}   => [qw{ test_standard_cli }],
+    );
 
-  MODULE:
-    for my $module (@modules) {
-        require_ok($module) or BAIL_OUT q{Cannot load} . $SPACE . $module;
-    }
+    test_import( { perl_module_href => \%perl_module, } );
 }
 
-use MIP::Program::Qc::Multiqc qw{ multiqc };
-use MIP::Test::Commands qw{ test_function };
+use MIP::Program::Multiqc qw{ multiqc };
 
 diag(   q{Test multiqc from Multiqc v}
-      . $MIP::Program::Qc::Multiqc::VERSION
+      . $MIP::Program::Multiqc::VERSION
       . $COMMA
       . $SPACE . q{Perl}
       . $SPACE
@@ -99,9 +63,9 @@ diag(   q{Test multiqc from Multiqc v}
 my @function_base_commands = qw{ multiqc };
 
 my %base_argument = (
-    stdoutfile_path => {
-        input           => q{stdoutfile.test},
-        expected_output => q{1> stdoutfile.test},
+    filehandle => {
+        input           => undef,
+        expected_output => \@function_base_commands,
     },
     stderrfile_path => {
         input           => q{stderrfile.test},
@@ -111,9 +75,9 @@ my %base_argument = (
         input           => q{stderrfile.test},
         expected_output => q{2>> stderrfile.test},
     },
-    filehandle => {
-        input           => undef,
-        expected_output => \@function_base_commands,
+    stdoutfile_path => {
+        input           => q{stdoutfile.test},
+        expected_output => q{1> stdoutfile.test},
     },
 );
 
@@ -144,45 +108,12 @@ foreach my $argument_href (@arguments) {
     my @commands = test_function(
         {
             argument_href              => $argument_href,
-            required_argument_href     => \%required_argument,
-            module_function_cref       => $module_function_cref,
-            function_base_commands_ref => \@function_base_commands,
             do_test_base_command       => 1,
+            function_base_commands_ref => \@function_base_commands,
+            module_function_cref       => $module_function_cref,
+            required_argument_href     => \%required_argument,
         }
     );
 }
 
 done_testing();
-
-######################
-####SubRoutines#######
-######################
-
-sub build_usage {
-
-## Function  : Build the USAGE instructions
-## Returns   :
-## Arguments : $program_name => Name of the script
-
-    my ($arg_href) = @_;
-
-    ## Default(s)
-    my $program_name;
-
-    my $tmpl = {
-        program_name => {
-            default     => basename($PROGRAM_NAME),
-            strict_type => 1,
-            store       => \$program_name,
-        },
-    };
-
-    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
-
-    return <<"END_USAGE";
- $program_name [options]
-    -vb/--verbose Verbose
-    -h/--help Display this help message
-    -v/--version Display version
-END_USAGE
-}