Merge pull request #1246 from Clinical-Genomics/feature/star_options

feat(star_options): updates star parameters
Clinical-Genomics · Dec 6, 2019 · 80b855f · 80b855f
2 parents 5831034 + c13075b
commit 80b855f
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Showing 3 changed files with 23 additions and 29 deletions.
diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
@@ -299,19 +299,19 @@ align_intron_max:
   associated_recipe:
     - star_aln
   data_type: SCALAR
-  default: 100000
+  mandatory: no
   type: recipe_argument
 align_mates_gap_max:
   associated_recipe:
     - star_aln
   data_type: SCALAR
-  default: 100000
+  mandatory: no
   type: recipe_argument
 align_sjdb_overhang_min:
   associated_recipe:
     - star_aln
   data_type: SCALAR
-  default: 10
+  mandatory: no
   type: recipe_argument
 chim_junction_overhang_min:
   associated_recipe:
@@ -329,7 +329,7 @@ chim_out_type:
   associated_recipe:
     - star_aln
   data_type: SCALAR
-  default: WithinBAM SoftClip 
+  default: WithinBAM SoftClip
   type: recipe_argument
 pe_overlap_nbases_min:
   associated_recipe:

diff --git a/lib/MIP/Program/Star.pm b/lib/MIP/Program/Star.pm
@@ -25,15 +25,15 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.03;
+    our $VERSION = 1.04;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ star_aln star_genome_generate };
 }
 
 sub star_aln {
 
-## Function  : Perl wrapper for STAR v2.5.3a.
+## Function  : Perl wrapper for STAR v2.7.3a.
 ## Returns   : @commands
 ## Arguments : $align_intron_max           => Maximum intron size
 ##           : $align_mates_gap_max        => Maximum gap between two mates
@@ -60,49 +60,45 @@ sub star_aln {
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
+    my $align_intron_max;
+    my $align_mates_gap_max;
+    my $align_sjdb_overhang_min;
     my $filehandle;
     my $chim_out_type;
+    my $chim_junction_overhang_min;
+    my $chim_segment_min;
     my $genome_dir_path;
     my $infile_paths_ref;
+    my $limit_bam_sort_ram;
     my $outfile_name_prefix;
     my $pe_overlap_nbases_min;
     my $stderrfile_path;
     my $stderrfile_path_append;
     my $stdoutfile_path;
+    my $thread_number;
 
     ## Default(s)
-    my $align_intron_max;
-    my $align_mates_gap_max;
-    my $align_sjdb_overhang_min;
-    my $chim_junction_overhang_min;
-    my $chim_segment_min;
     my $chim_segment_read_gap_max;
-    my $limit_bam_sort_ram;
     my $out_sam_strand_field;
     my $out_sam_type;
     my $quant_mode;
     my $read_files_command;
-    my $thread_number;
     my $two_pass_mode;
 
     my $tmpl = {
         align_intron_max => {
-            default     => 100_000,
             store       => \$align_intron_max,
             strict_type => 1,
         },
         align_mates_gap_max => {
-            default     => 100_000,
             store       => \$align_mates_gap_max,
             strict_type => 1,
         },
         align_sjdb_overhang_min => {
-            default     => 10,
             store       => \$align_sjdb_overhang_min,
             strict_type => 1,
         },
         chim_junction_overhang_min => {
-            default     => 12,
             store       => \$chim_junction_overhang_min,
             strict_type => 1,
         },
@@ -117,7 +113,6 @@ sub star_aln {
             strict_type => 1,
         },
         chim_segment_min => {
-            default     => 12,
             store       => \$chim_segment_min,
             strict_type => 1,
         },
@@ -143,7 +138,6 @@ sub star_aln {
             strict_type => 1,
         },
         limit_bam_sort_ram => {
-            default     => 315_321_372_30,
             store       => \$limit_bam_sort_ram,
             strict_type => 1,
         },
@@ -192,8 +186,7 @@ sub star_aln {
             strict_type => 1,
         },
         thread_number => {
-            allow       => qr/ ^\d+$ /xms,
-            default     => 16,
+            allow       => qr/ \A \d+ \z /xms,
             store       => \$thread_number,
             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 = 1.14;
+    our $VERSION = 1.15;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_star_aln };
@@ -279,13 +279,14 @@ sub analysis_star_aln {
                   $active_parameter_href->{align_sjdb_overhang_min},
                 chim_junction_overhang_min =>
                   $active_parameter_href->{chim_junction_overhang_min},
-                chim_out_type       => $active_parameter_href->{chim_out_type},
-                chim_segment_min    => $active_parameter_href->{chim_segment_min},
-                genome_dir_path     => $referencefile_dir_path,
-                infile_paths_ref    => \@fastq_files,
-                outfile_name_prefix => $outfile_path_prefix . $DOT,
-                thread_number       => $recipe_resource{core_number},
-                two_pass_mode       => $active_parameter_href->{two_pass_mode},
+                chim_out_type         => $active_parameter_href->{chim_out_type},
+                chim_segment_min      => $active_parameter_href->{chim_segment_min},
+                genome_dir_path       => $referencefile_dir_path,
+                infile_paths_ref      => \@fastq_files,
+                outfile_name_prefix   => $outfile_path_prefix . $DOT,
+                pe_overlap_nbases_min => $active_parameter_href->{pe_overlap_nbases_min},
+                thread_number         => $recipe_resource{core_number},
+                two_pass_mode         => $active_parameter_href->{two_pass_mode},
             },
         );
         say {$filehandle} $NEWLINE;