No need to update reference fasta location

CoverageProfiler/CoverageProfiler.wdl

@@ -47,14 +47,8 @@ workflow coverageProfile {
         # Create directories for input, output, reference localization
         mkdir input
         mkdir output
-        mkdir reference
 
-        # Localize Reference Files and BAM
-        mv ~{referenceFasta} reference/reference.fasta
-        mv ~{referenceDict} reference/reference.dict
-        mv ~{referenceFai} reference/reference.fai
         mv ~{alignedBam} input/~{sampleName}.bam
-
         # Index BAM file
         gatk BuildBamIndex \
             --INPUT input/~{sampleName}.bam
@@ -63,7 +57,7 @@ workflow coverageProfile {
         gatk --java-options "-Xmx~{command_mem_mb}m" DepthOfCoverage \
             -L ~{intervals} \
             --input input/~{sampleName}.bam \
-            --reference reference/reference.fasta \
+            --reference ~{referenceFasta} \
             --output output/~{sampleName}
 
         cat output/~{sampleName}.sample_interval_summary | awk 'BEGIN {FS = ","}{print $3}' | tail -n 1 > output/mean_coverage.txt