fix(svdb and gatk): Modified svdb and gatk recipe

- Allow emptry string out tag vcf keys with svdb
- Fixed contig specific genomicsdb to prevent collisions

definitions/rd_dna_parameters.yaml

@@ -272,7 +272,7 @@ recipe_time:
     snpeff: 10
     sv_annotate: 2
     sv_combinevariantcallsets: 2
-    sv_rankvariant: 2
+    sv_rankvariant: 10
     sv_reformat: 1
     sv_varianteffectpredictor: 10
     sv_vcfparser: 2

lib/MIP/Recipes/Analysis/Gatk_genotypegvcfs.pm

@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.14;
+    our $VERSION = 1.15;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_gatk_genotypegvcfs };
@@ -244,6 +244,7 @@ sub analysis_gatk_genotypegvcfs {
         my @sample_vcf_path_lines;
         my $sample_name_map_path;
 
+      SAMPLE_ID:
         while ( my ( $sample_id_index, $sample_id ) =
             each @{ $active_parameter_href->{sample_ids} } )
         {
@@ -291,10 +292,12 @@ sub analysis_gatk_genotypegvcfs {
             );
 
         }
+        my $genomicsdb_file_path =
+          $outfile_path_prefix . $UNDERSCORE . q{DB} . $UNDERSCORE . $contig;
         gatk_genomicsdbimport(
             {
                 FILEHANDLE                => $FILEHANDLE,
-                genomicsdb_workspace_path => $outfile_path_prefix . $UNDERSCORE . q{DB},
+                genomicsdb_workspace_path => $genomicsdb_file_path,
                 intervals_ref             => [$contig],
                 infile_paths_ref          => \@genotype_infile_paths,
                 java_use_large_pages => $active_parameter_href->{java_use_large_pages},
@@ -317,8 +320,8 @@ sub analysis_gatk_genotypegvcfs {
                 FILEHANDLE => $FILEHANDLE,
                 include_nonvariant_sites =>
                   $active_parameter_href->{gatk_genotypegvcfs_all_sites},
-                infile_path   => q{gendb://} . $outfile_path_prefix . $UNDERSCORE . q{DB},
-                intervals_ref => [$contig],
+                infile_path          => q{gendb://} . $genomicsdb_file_path,
+                intervals_ref        => [$contig],
                 java_use_large_pages => $active_parameter_href->{java_use_large_pages},
                 memory_allocation    => q{Xmx} . $JAVA_MEMORY_ALLOCATION . q{g},
                 outfile_path         => $outfile_path{$contig},

lib/MIP/Recipes/Analysis/Sv_annotate.pm

@@ -27,7 +27,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.10;
+    our $VERSION = 1.11;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_sv_annotate };
@@ -279,10 +279,11 @@ sub analysis_sv_annotate {
             ## Get parameters
 # Split query_db_tag to decide svdb input query fields
 # FORMAT: filename|OUT_FREQUENCY_INFO_KEY|OUT_ALLELE_COUNT_INFO_KEY|IN_FREQUENCY_INFO_KEY|IN_ALLELE_COUNT_INFO_KEY
-            my (
-                $query_db_tag,     $out_frequency_tag, $out_allele_count_tag,
-                $in_frequency_tag, $in_allele_count_tag
-            ) = split /[|]/sxm, $query_db_tag_info;
+            my ( $query_db_tag, $out_frequency_tag_suffix, $out_allele_count_tag_suffix,
+                $in_frequency_tag, $in_allele_count_tag )
+              = split /[|]/sxm, $query_db_tag_info;
+            my $out_frequency_tag    = $out_frequency_tag_suffix    ||= $EMPTY_STR;
+            my $out_allele_count_tag = $out_allele_count_tag_suffix ||= $EMPTY_STR;
 
             svdb_query(
                 {

mip-check

@@ -68,7 +68,7 @@ do
 	fi
 
     ## Run perltidy
-    if [[ "$(perltidy --maximum-line-length=90 --iterations=2 -b -bext='/' $infile -gt 0 ]]; then
+    if [[ "$(perltidy --maximum-line-length=90 --iterations=2 -b -bext='/' $infile)" -gt 0 ]]; then
 	echo >&2 "There was an error when running perltidy on $infile; please see the error file for more info"
            exit 1
     fi