Merge branch 'release/mip9.0.4' into develop

CHANGELOG.md

@@ -2,6 +2,11 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [9.0.4]
+- Increased memory allocation for samtools_subsample_mt
+- Check that vep plugin paths exists prior to executing mip
+- Cd into cadd temp directory before executing cadd in order to escape snakemake lock errors
+
 ## [9.0.3]
 - Changed path and name of slurm job ids file to facilitate analysis monitoring
 - SpliceAI annotation with VEP instead of vcfanno

definitions/rd_dna_parameters.yaml

@@ -228,7 +228,7 @@ recipe_memory:
     rhocall_ar: 2
     rhocall_viz: 5
     sambamba_depth: 10
-    samtools_subsample_mt: 2
+    samtools_subsample_mt: 4
     split_fastq_file: 2
     sv_annotate: 7
     sv_reformat: 24

lib/MIP/Active_parameter.pm

@@ -1270,8 +1270,9 @@ sub parse_vep_plugin {
 
         check_vep_plugin(
             {
-                parameter_name  => $parameter_name,
-                vep_plugin_href => \%{ $active_parameter_href->{$parameter_name} },
+                parameter_name       => $parameter_name,
+                vep_plugin_href      => \%{ $active_parameter_href->{$parameter_name} },
+                vep_plugins_dir_path => $active_parameter_href->{vep_plugins_dir_path},
             }
         );
     }

lib/MIP/Constants.pm

@@ -20,7 +20,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.24;
+    our $VERSION = 1.25;
 
     # Functions and variables which can be optionally exported
 
@@ -80,7 +80,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{v9.0.3};
+Readonly our $MIP_VERSION => q{v9.0.4};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

lib/MIP/Recipes/Analysis/Cadd.pm

@@ -123,7 +123,7 @@ sub analysis_cadd {
 
     use MIP::Get::File qw{ get_io_files };
     use MIP::Get::Parameter qw{ get_recipe_attributes get_recipe_resources };
-    use MIP::Program::Gnu::Bash qw{ gnu_export gnu_unset };
+    use MIP::Program::Gnu::Bash qw{ gnu_cd gnu_export gnu_unset };
     use MIP::Program::Gnu::Coreutils qw{ gnu_mkdir };
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Program::Bcftools qw{ bcftools_annotate bcftools_concat bcftools_view };
@@ -325,6 +325,16 @@ sub analysis_cadd {
         );
         print {$xargsfilehandle} $SEMICOLON . $SPACE;
 
+        ## Attempt to escape snakemake lock
+        gnu_cd(
+            {
+                filehandle             => $xargsfilehandle,
+                directory_path         => $temp_outdir_path{$contig},
+                stderrfile_path_append => $stderrfile_path,
+            }
+        );
+        print {$xargsfilehandle} $SEMICOLON . $SPACE;
+
         cadd(
             {
                 filehandle             => $xargsfilehandle,

lib/MIP/Vep.pm

@@ -4,7 +4,7 @@ use 5.026;
 use Carp;
 use charnames qw{ :full :short };
 use English qw{ -no_match_vars };
-use File::Spec::Functions qw{ catdir };
+use File::Spec::Functions qw{ catdir catfile };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
 use strict;
@@ -24,7 +24,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.02;
+    our $VERSION = 1.03;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
@@ -187,16 +187,18 @@ sub check_vep_custom_annotation {
 
 sub check_vep_plugin {
 
-## Function : Check VEP plugin options
+## Function : Check VEP plugins and options
 ## Returns  : 0 or 1
-## Arguments: $parameter_name  => Parameter name
-##          : $vep_plugin_href => VEP plugin annotation {REF}
+## Arguments: $parameter_name       => Parameter name
+##          : $vep_plugin_href      => VEP plugin annotation {REF}
+##          : $vep_plugins_dir_path => VEP plugin dir path
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
     my $parameter_name;
     my $vep_plugin_href;
+    my $vep_plugins_dir_path;
 
     my $tmpl = {
         parameter_name => {
@@ -211,6 +213,12 @@ sub check_vep_plugin {
             store       => \$vep_plugin_href,
             strict_type => 1,
         },
+        vep_plugins_dir_path => {
+            defined     => 1,
+            required    => 1,
+            store       => \$vep_plugins_dir_path,
+            strict_type => 1,
+        },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
@@ -226,6 +234,15 @@ sub check_vep_plugin {
         my $err_msg = $plugin . q{ Is not a hash ref for vep_plugin};
         croak($err_msg) if ( ref $value_href ne q{HASH} );
 
+        check_filesystem_objects_and_index_existance(
+            {
+                object_name    => $plugin,
+                object_type    => q{file},
+                parameter_name => $parameter_name,
+                path           => catfile( $vep_plugins_dir_path, $plugin . q{.pm} ),
+            }
+        );
+
         next PLUGIN if ( not exists $value_href->{exist_check} );
 
       OBJECT:

t/check_vep_plugin.t

@@ -6,7 +6,7 @@ use charnames qw{ :full :short };
 use Cwd;
 use English qw{ -no_match_vars };
 use File::Basename qw{ dirname };
-use File::Spec::Functions qw{ catdir };
+use File::Spec::Functions qw{ catdir catfile };
 use FindBin qw{ $Bin };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
@@ -23,10 +23,12 @@ use Test::Trap;
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Io::Read qw{ read_from_file };
 use MIP::Test::Fixtures qw{ test_log test_standard_cli };
+use MIP::Update::Parameters qw{ update_with_dynamic_config_parameters };
 
 my $VERBOSE = 1;
-our $VERSION = 1.01;
+our $VERSION = 1.02;
 
 $VERBOSE = test_standard_cli(
     {
@@ -62,30 +64,42 @@ diag(   q{Test check_vep_plugin from Vep.pm v}
 
 my $log = test_log( { no_screen => 1, } );
 
-## Given an undefine vep plugin hash
+## Read config for most up to date format
+my %rd_dna_config = read_from_file(
+    {
+        format => q{yaml},
+        path   => catfile( dirname($Bin), qw{ templates mip_rd_dna_config.yaml } ),
+    }
+);
+my %dynamic_parameter =
+  ( cluster_constant_path => catfile( dirname($Bin), qw{ t data } ), );
+update_with_dynamic_config_parameters(
+    {
+        active_parameter_href  => \%rd_dna_config,
+        dynamic_parameter_href => \%dynamic_parameter,
+    }
+);
+## Given an undefined vep plugin hash
 my %vep_plugin;
 
 my $is_not_ok = check_vep_plugin(
     {
-        parameter_name  => q{vep_plugin},
-        vep_plugin_href => \%vep_plugin,
+        parameter_name       => q{vep_plugin},
+        vep_plugin_href      => \%vep_plugin,
+        vep_plugins_dir_path => $rd_dna_config{vep_plugins_dir_path},
     }
 );
 ## Then there is nothing to check - return false
 is( $is_not_ok, 0, q{Nothing to check} );
 
-%vep_plugin = (
-    dbNSFP => {
-        exists_check => q{directory},
-        path         => cwd(),
-        parameters   => [qw{ param_1 param_2 }],
-    },
-);
+## Given a plugin hash
+$vep_plugin{dbNSFP} = $rd_dna_config{vep_plugin}{dbNSFP};
 
 my $is_ok = check_vep_plugin(
     {
-        parameter_name  => q{vep_plugin},
-        vep_plugin_href => \%vep_plugin,
+        parameter_name       => q{vep_plugin},
+        vep_plugin_href      => \%vep_plugin,
+        vep_plugins_dir_path => $rd_dna_config{vep_plugins_dir_path},
     }
 );
 
@@ -98,8 +112,9 @@ $vep_plugin{not_valid_annotation} = [q{not_a_valid_ref}];
 trap {
     check_vep_plugin(
         {
-            parameter_name  => q{vep_plugin},
-            vep_plugin_href => \%vep_plugin,
+            parameter_name       => q{vep_plugin},
+            vep_plugin_href      => \%vep_plugin,
+            vep_plugins_dir_path => $rd_dna_config{vep_plugins_dir_path},
         }
     )
 };
@@ -110,4 +125,19 @@ like( $trap->die, qr/Is\s+not\s+a/xms, q{Not a hash ref} );
 
 delete $vep_plugin{not_valid_annotation};
 
+## Given a plugin that is missing
+$vep_plugin{MockPlugin} = $rd_dna_config{vep_plugin}{ExACpLI};
+trap {
+    check_vep_plugin(
+        {
+            parameter_name       => q{vep_plugin},
+            vep_plugin_href      => \%vep_plugin,
+            vep_plugins_dir_path => $rd_dna_config{vep_plugins_dir_path},
+        }
+    )
+};
+
+## Then exit
+is( $trap->leaveby, q{exit}, q{Exit if the plugin doesn't exist } );
+
 done_testing();

t/parse_vep_plugin.t

@@ -6,7 +6,7 @@ use charnames qw{ :full :short };
 use Cwd;
 use English qw{ -no_match_vars };
 use File::Basename qw{ dirname };
-use File::Spec::Functions qw{ catdir };
+use File::Spec::Functions qw{ catdir catfile };
 use FindBin qw{ $Bin };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
@@ -23,7 +23,9 @@ use Test::Trap;
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Io::Read qw{ read_from_file };
 use MIP::Test::Fixtures qw{ test_log test_standard_cli };
+use MIP::Update::Parameters qw{ update_with_dynamic_config_parameters };
 
 my $VERBOSE = 1;
 our $VERSION = 1.00;
@@ -62,21 +64,34 @@ diag(   q{Test parse_vep_plugin from Active_parameter.pm v}
 
 my $log = test_log( { no_screen => 1, } );
 
-## Given a vep plugin hash
-my %active_parameter_href = (
+## Read config for most up to date format
+my %rd_dna_config = read_from_file(
+    {
+        format => q{yaml},
+        path   => catfile( dirname($Bin), qw{ templates mip_rd_dna_config.yaml } ),
+    }
+);
+my %dynamic_parameter =
+  ( cluster_constant_path => catfile( dirname($Bin), qw{ t data } ), );
+update_with_dynamic_config_parameters(
+    {
+        active_parameter_href  => \%rd_dna_config,
+        dynamic_parameter_href => \%dynamic_parameter,
+    }
+);
+
+## Given a plugin hash
+my %active_parameter = (
     vep_plugin => {
-        dbNSFP => {
-            exists_check => q{directory},
-            path         => cwd(),
-            parameters   => [qw{ param_1 param_2 }],
-        },
+        dbNSFP => $rd_dna_config{vep_plugin}{dbNSFP},
     },
+    vep_plugins_dir_path => $rd_dna_config{vep_plugins_dir_path},
 );
-my @mip_vep_plugins = qw{ vep_plugin };
 
-my $is_ok = parse_vep_plugin(
+my @mip_vep_plugins = qw{ vep_plugin };
+my $is_ok           = parse_vep_plugin(
     {
-        active_parameter_href => \%active_parameter_href,
+        active_parameter_href => \%active_parameter,
         mip_vep_plugins_ref   => \@mip_vep_plugins,
     }
 );