Merge 8fe83f9 into 53a6616

definitions/rd_dna_initiation_map.yaml

@@ -54,6 +54,7 @@ CHAIN_ALL:
       - retroseq
       - me_merge_vcfs
       - me_annotate
+      - me_varianteffectpredictor
   - CHAIN_MAIN:
     # PARALLEL chains, which inherit from MAIN in initiation, but are merged back to CHAIN_MAIN after execution
     - PARALLEL:

definitions/rd_dna_parameters.yaml

@@ -229,6 +229,7 @@ recipe_core_number:
     me_annotate: 2
     me_merge_bam: 5
     me_merge_vcfs: 2
+    me_varianteffectpredictor: 4
     mitodel: 1
     mt_annotation: 1
     multiqc_ar: 1
@@ -363,6 +364,7 @@ recipe_time:
     me_annotate: 2
     me_merge_bam: 5
     me_merge_vcfs: 2
+    me_varianteffectpredictor: 3
     mitodel: 2
     mt_annotation: 1
     multiqc_ar: 5
@@ -1359,6 +1361,19 @@ me_annotate_exons_bed:
   is_reference: 1
   reference: reference_dir
   type: path
+me_varianteffectpredictor:
+  analysis_mode: case
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 1
+  file_tag: _vep
+  outfile_suffix: ".vcf.gz"
+  program_executables:
+    - bcftools
+    - tabix
+    - vep
+  type: recipe
 ## GATK CollectReadCounts
 gatk_collectreadcounts:
   analysis_mode: sample

lib/MIP/Cli/Mip/Analyse/Rd_dna.pm

@@ -1245,6 +1245,15 @@ q{Default: hgvs, symbol, numbers, sift, polyphen, humdiv, domains, protein, ccds
         )
     );
 
+    option(
+        q{me_varianteffectpredictor} => (
+            cmd_tags      => [q{Analysis recipe switch}],
+            documentation => q{Annotate mobile elements with VEP},
+            is            => q{rw},
+            isa           => enum( [ 0, 1, 2 ] ),
+        )
+    );
+
     option(
         q{gatk_haplotypecaller} => (
             cmd_tags      => [q{Analysis recipe switch}],

lib/MIP/Program/Vep.pm

@@ -39,6 +39,7 @@ sub variant_effect_predictor {
 ## Arguments: $assembly                => Assembly version to use
 ##          : $buffer_size             => Sets the internal buffer size, corresponding to the number of variants that are read in to memory simultaneously
 ##          : $cache_directory         => VEP chache directory
+##          : $compress_output         => Compress output
 ##          : $custom_annotations_ref  => Custom annotations {REF}
 ##          : $distance                => Modify the distance up and/or downstream between a variant and a transcript for which VEP will assign the upstream_gene_variant or downstream_gene_variant consequences
 ##          : $filehandle              => Filehandle to write to
@@ -65,6 +66,7 @@ sub variant_effect_predictor {
     my $assembly;
     my $buffer_size;
     my $cache_directory;
+    my $compress_output;
     my $custom_annotations_ref;
     my $filehandle;
     my $infile_path;
@@ -102,6 +104,11 @@ sub variant_effect_predictor {
             store       => \$cache_directory,
             strict_type => 1,
         },
+        compress_output => {
+            allow       => [ undef, 0, 1 ],
+            store       => \$compress_output,
+            strict_type => 1,
+        },
         custom_annotations_ref => {
             default     => [],
             store       => \$custom_annotations_ref,
@@ -225,6 +232,10 @@ sub variant_effect_predictor {
 
         push @commands, q{--dir_cache} . $SPACE . $cache_directory;
     }
+    if ($compress_output) {
+
+        push @commands, q{--compress_output} . $SPACE . q{bgzip};
+    }
     if ($infile_format) {
 
         push @commands, q{--format} . $SPACE . $infile_format;
@@ -259,8 +270,7 @@ sub variant_effect_predictor {
     }
     if ( @{$custom_annotations_ref} ) {
 
-        push @commands, q{--custom} . $SPACE . join q{ --custom },
-          @{$custom_annotations_ref};
+        push @commands, q{--custom} . $SPACE . join q{ --custom }, @{$custom_annotations_ref};
     }
     if ( @{$vep_features_ref} ) {
 
@@ -353,11 +363,10 @@ sub variant_effect_predictor_install {
             store       => \$species_ref,
             strict_type => 1,
         },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
-        stdoutfile_path => { store => \$stdoutfile_path, strict_type => 1, },
-        version         => { store => \$version,         strict_type => 1, },
+        stderrfile_path        => { store => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
+        stdoutfile_path        => { store => \$stdoutfile_path,        strict_type => 1, },
+        version                => { store => \$version,                strict_type => 1, },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};