Remove directory level from complex Manta tars

TinyResolve produces tar files with a top level directory and all VCFs
inside the directory. However, the ClusterBatch workflow expects tar
files with all VCFs placed at the top level. This commit updates the
TinyResolve workflow to produce tar files with all VCFs at the top
level to be compatible with ClusterBatch.

wdl/TinyResolve.wdl

@@ -192,14 +192,22 @@ task ConcatTars {
     while read -r tl; do
       tar --extract --file "${tl}" --directory manta_tloc
     done < '~{write_lines(manta_tloc_tars)}'
-    tar --create --gzip --file manta_tloc.tar.gz manta_tloc
+    pushd manta_tloc
+    find . -type f -name '*.vcf.gz' > manifest.list
+    popd
+    tar --create --gzip --file manta_tloc.tar.gz --directory manta_tloc \
+      --files-from manta_tloc/manifest.list
     rm -rf manta_tloc
 
     mkdir manta_unresolved
     while read -r ur; do
       tar --extract --file "${ur}" --directory manta_unresolved
     done < '~{write_lines(manta_unresolved_tars)}'
-    tar --create --gzip --file manta_unresolved.tar.gz manta_unresolved
+    pushd manta_unresolved
+    find . -type f -name '*.vcf.gz' > manifest.list
+    popd
+    tar --create --gzip --file manta_unresolved.tar.gz \
+      --directory manta_unresolved --files-from manta_unresolved/manifest.list
   >>>
 
   runtime {