Merge 0dc9a36 into f18b023

Clinical-Genomics · Dec 3, 2020 · b4986f1 · b4986f1
2 parents f18b023 + 0dc9a36
commit b4986f1
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Showing 5 changed files with 36 additions and 20 deletions.
diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
@@ -83,6 +83,7 @@ library_type:
   associated_recipe:
     - genebody_coverage
     - picardtools_collectrnaseqmetrics
+    - star_aln
     - stringtie_ar
   data_type: SCALAR
   default: reverse_stranded

diff --git a/lib/MIP/Program/Star.pm b/lib/MIP/Program/Star.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.07;
+    our $VERSION = 1.08;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ star_aln star_genome_generate };
@@ -222,8 +222,8 @@ sub star_aln {
             strict_type => 1,
         },
         out_sam_strand_field => {
-            allow       => [qw{ None intronMotif }],
-            default     => q{intronMotif},
+            allow       => [ undef, qw{ None intronMotif } ],
+            default     => q{None},
             store       => \$out_sam_strand_field,
             strict_type => 1,
         },

diff --git a/lib/MIP/Recipes/Analysis/Star_aln.pm b/lib/MIP/Recipes/Analysis/Star_aln.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.19;
+    our $VERSION = 1.20;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_star_aln analysis_star_aln_mixed };
@@ -290,6 +290,8 @@ sub analysis_star_aln {
         $active_parameter_href->{star_aln_reference_genome}
       . $file_info_href->{star_aln_reference_genome}[0];
 
+    my $out_sam_strand_field =
+      $active_parameter_href->{library_type} eq q{unstranded} ? q{intronMotif} : undef;
     star_aln(
         {
             align_intron_max        => $active_parameter_href->{align_intron_max},
@@ -303,6 +305,7 @@ sub analysis_star_aln {
             genome_dir_path       => $referencefile_dir_path,
             infile_paths_ref      => \@fastq_files,
             out_sam_attr_rgline   => $out_sam_attr_rgline,
+            out_sam_strand_field  => $out_sam_strand_field,
             outfile_name_prefix   => $outfile_path_prefix . $DOT,
             pe_overlap_nbases_min => $active_parameter_href->{pe_overlap_nbases_min},
             thread_number         => $recipe_resource{core_number},
@@ -641,6 +644,11 @@ sub analysis_star_aln_mixed {
                 separator        => $SPACE,
             }
         );
+
+        my $out_sam_strand_field =
+          $active_parameter_href->{library_type} eq q{unstranded}
+          ? q{intronMotif}
+          : undef;
         star_aln(
             {
                 filehandle          => $filehandle,
@@ -655,6 +663,7 @@ sub analysis_star_aln_mixed {
                 genome_dir_path       => $referencefile_dir_path,
                 infile_paths_ref      => \@fastq_files,
                 out_sam_attr_rgline   => $out_sam_attr_rgline,
+                out_sam_strand_field  => $out_sam_strand_field,
                 outfile_name_prefix   => $outfile_path_prefix . $DOT,
                 pe_overlap_nbases_min => $active_parameter_href->{pe_overlap_nbases_min},
                 thread_number         => $recipe_resource{core_number},

diff --git a/t/analysis_star_aln.t b/t/analysis_star_aln.t
@@ -21,10 +21,11 @@ use Test::Trap;
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COLON $COMMA $SPACE };
-use MIP::Test::Fixtures qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli };
+use MIP::Test::Fixtures
+  qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli };
 
 my $VERBOSE = 1;
-our $VERSION = 1.03;
+our $VERSION = 1.04;
 
 $VERBOSE = test_standard_cli(
     {
@@ -41,7 +42,8 @@ BEGIN {
 ## Modules with import
     my %perl_module = (
         q{MIP::Recipes::Analysis::Star_aln} => [qw{ analysis_star_aln }],
-        q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli }],
+        q{MIP::Test::Fixtures} =>
+          [qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli }],
     );
 
     test_import( { perl_module_href => \%perl_module, } );
@@ -77,6 +79,7 @@ my $sample_id = $active_parameter{sample_ids}[0];
 $active_parameter{platform}                  = q{ILLUMINA};
 $active_parameter{star_aln_reference_genome} = q{a_dir};
 $active_parameter{two_pass_mode}             = q{Basic};
+$active_parameter{library_type}              = q{unstranded};
 
 my %file_info = test_mip_hashes(
     {
@@ -98,11 +101,11 @@ my %parameter = test_mip_hashes(
 
 test_add_io_for_recipe(
     {
-        file_info_href    => \%file_info,
-        id                => $sample_id,
-        parameter_href    => \%parameter,
-        recipe_name       => $recipe_name,
-        step              => q{fastq},
+        file_info_href => \%file_info,
+        id             => $sample_id,
+        parameter_href => \%parameter,
+        recipe_name    => $recipe_name,
+        step           => q{fastq},
     }
 );
 

diff --git a/t/analysis_star_aln_mixed.t b/t/analysis_star_aln_mixed.t
@@ -21,10 +21,11 @@ use Test::Trap;
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COLON $COMMA $SPACE };
-use MIP::Test::Fixtures qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli };
+use MIP::Test::Fixtures
+  qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli };
 
 my $VERBOSE = 1;
-our $VERSION = 1.02;
+our $VERSION = 1.03;
 
 $VERBOSE = test_standard_cli(
     {
@@ -41,7 +42,8 @@ BEGIN {
 ## Modules with import
     my %perl_module = (
         q{MIP::Recipes::Analysis::Star_aln} => [qw{ analysis_star_aln_mixed }],
-        q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli }],
+        q{MIP::Test::Fixtures} =>
+          [qw{ test_add_io_for_recipe test_log test_mip_hashes test_standard_cli }],
     );
 
     test_import( { perl_module_href => \%perl_module, } );
@@ -77,6 +79,7 @@ my $sample_id = $active_parameter{sample_ids}[0];
 $active_parameter{platform}                  = q{ILLUMINA};
 $active_parameter{star_aln_reference_genome} = q{a_dir};
 $active_parameter{two_pass_mode}             = q{Basic};
+$active_parameter{library_type}              = q{reverse_stranded};
 
 my %file_info = test_mip_hashes(
     {
@@ -100,11 +103,11 @@ my %parameter = test_mip_hashes(
 
 test_add_io_for_recipe(
     {
-        file_info_href    => \%file_info,
-        id                => $sample_id,
-        parameter_href    => \%parameter,
-        recipe_name       => $recipe_name,
-        step              => q{bam},
+        file_info_href => \%file_info,
+        id             => $sample_id,
+        parameter_href => \%parameter,
+        recipe_name    => $recipe_name,
+        step           => q{bam},
     }
 );