Added snpeff_db_identifier for Functional annotation. (#482)

- Removed hard-coded plasmodium snpeff database specification. - Added new input `snpeff_db_identifier` for a snpeff database specification to SRJointCallGVCFsWithGenomicsDB and FunctionalAnnotation`
broadinstitute · Dec 13, 2024 · b169a39 · b169a39
1 parent 076f587
commit b169a39
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl b/wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl
@@ -98,6 +98,7 @@ workflow SRJointCallGVCFsWithGenomicsDB {
         Array[String]? annotation_bed_file_annotation_names
 
         File? snpeff_db
+        String? snpeff_db_identifier
 
         File? interval_list
 
@@ -369,7 +370,8 @@ workflow SRJointCallGVCFsWithGenomicsDB {
             call FUNK.FunctionallyAnnotateVariants as FunctionallyAnnotate {
                 input:
                     vcf = recalibrated_vcf,
-                    snpeff_db = select_first([snpeff_db])
+                    snpeff_db = select_first([snpeff_db]),
+                    snpeff_db_identifier = select_first([snpeff_db_identifier])
             }
         }
 

diff --git a/wdl/tasks/TertiaryAnalysis/FunctionalAnnotation.wdl b/wdl/tasks/TertiaryAnalysis/FunctionalAnnotation.wdl
@@ -7,6 +7,8 @@ task FunctionallyAnnotateVariants {
         File vcf
         File snpeff_db
 
+        String snpeff_db_identifier
+
         RuntimeAttr? runtime_attr_override
     }
 
@@ -21,7 +23,7 @@ task FunctionallyAnnotateVariants {
         /snpEff/scripts/snpEff ann -v \
             -c $PWD/snpeff_db/snpEff.config \
             -dataDir $PWD/snpeff_db/data \
-            PlasmoDB-61_Pfalciparum3D7_Genome \
+            ~{snpeff_db_identifier} \
             ~{vcf} | bgzip > ~{prefix}.annotated.vcf.gz
 
         mv snpEff_summary.html ~{prefix}.snpEff_summary.html