handle the case where there are no variants to shard (#63)

broadinstitute · Oct 15, 2020 · b3393c5 · b3393c5
1 parent 6f3a808
commit b3393c5
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/wdl/ChromosomeAlleleFrequencies.wdl b/wdl/ChromosomeAlleleFrequencies.wdl
@@ -105,7 +105,11 @@ task ShardVcf {
       ~{contig}.vcf.gz \
       ~{sv_per_shard} \
       "vcf.shard."
-
+
+    # if there were no shards created just make an empty one
+    if [ ! -e vcf.shard.000000.vcf.gz ]; then
+      cp ~{contig}.vcf.gz vcf.shard.000000.vcf.gz
+    fi
   >>>
 
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