only do cram qc if crams exist

Author: mmorgantaylor

pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl

@@ -7,7 +7,7 @@ workflow Glimpse2LowPassImputation {
 
         Array[String] contigs
 
-        # this is the path the a directory that contains sites vcf, sites tabke, and reference chunks file.  should end with a "/
+        # this is the path the a directory that contains sites vcf, sites table, and reference chunks file.  should end with a "/"
         String reference_panel_prefix
 
         File? input_vcf

pipelines/wdl/glimpse/low_pass_imputation/input_qc/LowPassImputationQC.wdl

@@ -30,7 +30,7 @@ workflow InputQC {
     }
 
     # validate that not more than one of these is provided
-    if ( (defined(crams) && defined(cram_manifest))) {
+    if ((defined(crams) && defined(cram_manifest))) {
         Boolean multiple_data_types_passes_qc = false
         String multiple_data_types_message = "Multiple input data types provided. Please provide only CRAM files (with corresponding CRAM index files and sample IDs) or a CRAM manifest."
     }
@@ -43,7 +43,7 @@ workflow InputQC {
         }
     }
 
-    Boolean do_cram_qc = select_first([ConvertCramManifestToCramArrays.passes_qc, true]) # only do cram QC if manifest conversion passed QC
+    Boolean do_cram_qc = select_first([ConvertCramManifestToCramArrays.passes_qc, defined(crams)]) # only do cram QC if manifest conversion passed QC
     
     # validations for array crams input
     if (do_cram_qc) {