remove in-case-of-fire step since subworkflow works much better

scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl

@@ -84,9 +84,6 @@ task ExtractAnAcAfFromVCF {
     String normalized_vcf_compressed = "normalized.vcf.gz"
     String normalized_vcf_indexed = "normalized.vcf.gz.tbi"
 
-    String output_directory_name = output_path + 'med/' + local_input_vcf
-
-
     # separate multi-allelic sites into their own lines, remove deletions and filtered sites and make a sites only vcf
     # while extracting and calculating the an/ac/af & sc by subpopulation into a tsv
     command <<<
@@ -171,17 +168,6 @@ task ExtractAnAcAfFromVCF {
         ## if we can spare the IO and want to pass a smaller file we can also drop the info field w bcftools annotate -x INFO
         bcftools index --tbi  ~{normalized_vcf_compressed}
 
-
-        ## To prevent premature failures from this brittle step, the output will be saved to GCP
-        ## in case of fire, there are 3 files that I really need:
-        # custom_annotations_file_name, normalized_vcf_compressed, normalized_vcf_indexed
-        ## and they will be loaded with gsutil commands
-        gsutil cp ~{custom_annotations_file_name} '~{output_directory_name}/~{custom_annotations_file_name}'
-        # gsutil cp count.txt '~{output_directory_name}/count.txt' ## maybe I'm okay with losing track of this
-        # gsutil cp track_dropped.tsv '~{output_directory_name}/track_dropped.tsv}' ## maybe I'm okay with losing track of this
-        gsutil cp ~{normalized_vcf_compressed} '~{output_directory_name}/~{normalized_vcf_compressed}'
-        gsutil cp ~{normalized_vcf_indexed} '~{output_directory_name}/~{normalized_vcf_indexed}'
-
     >>>
     # ------------------------------------------------
     # Runtime settings: