update options (#1959)

* update options

* update test

modules/genmod/compound/main.nf

@@ -24,6 +24,7 @@ process GENMOD_COMPOUND {
     genmod \\
         compound \\
         $args \\
+        --processes ${task.cpus} \\
         --outfile ${prefix}_compound.vcf \\
         $input_vcf
 

modules/genmod/models/main.nf

@@ -30,6 +30,7 @@ process GENMOD_MODELS {
         $args \\
         $pen_file \\
         $family_file \\
+        --processes ${task.cpus} \\
         --outfile ${prefix}_models.vcf \\
         $input_vcf
 

modules/genmod/score/main.nf

@@ -10,7 +10,6 @@ process GENMOD_SCORE {
     input:
     tuple val(meta), path(input_vcf)
     path (fam)
-    path (reduced_penetrance)
     path (score_config)
 
     output:
@@ -24,13 +23,11 @@ process GENMOD_SCORE {
     def args        = task.ext.args ?: ''
     def prefix      = task.ext.prefix ?: "${meta.id}"
     def family_file = fam ? "--family_file ${fam}" : ""
-    def pen_file    = reduced_penetrance ? "--reduced_penetrance ${reduced_penetrance}" : ""
     def config_file = score_config ? "--score_config ${score_config}" : ""
     """
     genmod \\
         score \\
         $args \\
-        $pen_file \\
         $family_file \\
         $config_file \\
         --outfile ${prefix}_score.vcf \\

modules/genmod/score/meta.yml

@@ -21,10 +21,6 @@ input:
       type: file
       description: vcf file
       pattern: "*.{vcf}"
-  - reduced_penetrance:
-      type: file
-      description: file with gene ids that have reduced penetrance
-      pattern: "*.{tsv}"
   - family_file:
       type: file
       description: ped file

tests/modules/genmod/score/main.nf

@@ -13,10 +13,10 @@ config = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkI
 
 workflow test_genmod_score {
 
-    GENMOD_SCORE    ( input, fam, [], config)
+    GENMOD_SCORE    ( input, fam, config)
 }
 
 workflow test_genmod_score_stub {
 
-    GENMOD_SCORE    ( input, fam, [], config)
+    GENMOD_SCORE    ( input, fam, config)
 }