Merge pull request #1007 from nextstrain/wdl/minor_edit

wdl: use cp instead of mv
nextstrain · Oct 1, 2022 · dc5d73b · dc5d73b
2 parents 26b64ea + b63b836
commit dc5d73b
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/workflow/wdl/tasks/ncov_ingest.wdl b/workflow/wdl/tasks/ncov_ingest.wdl
@@ -46,16 +46,16 @@ task gisaid_ingest {
 
       # Detect and decompress xz or zst files
       if [[ $NEXTCLADE_CACHE == *.xz ]]; then
-        mv ~{cache_nextclade_old} .
+        cp ~{cache_nextclade_old} .
         xz -T0 --decompress ~{basename(select_first([cache_nextclade_old,'']))}
         export NEXTCLADE_CACHE="~{basename(select_first([cache_nextclade_old,'']),'.xz')}"
       elif [[ $NEXTCLADE_CACHE == *.zst ]]; then
-        mv ~{cache_nextclade_old} .
+        cp ~{cache_nextclade_old} .
         zstd -T0 -d ~{basename(select_first([cache_nextclade_old,'']))}
         export NEXTCLADE_CACHE="~{basename(select_first([cache_nextclade_old,'']),'.zst')}"
       fi
 
-      mv $NEXTCLADE_CACHE ${NCOV_INGEST_DIR}/data/gisaid/nextclade_old.tsv
+      cp $NEXTCLADE_CACHE ${NCOV_INGEST_DIR}/data/gisaid/nextclade_old.tsv
       echo "nextclade_old.tsv has " `wc -l ${NCOV_INGEST_DIR}/data/gisaid/nextclade_old.tsv` " records."
     fi
 
@@ -175,16 +175,16 @@ task genbank_ingest {
 
       # Detect and decompress xz or zst files
       if [[ $NEXTCLADE_CACHE == *.xz ]]; then
-        mv ~{cache_nextclade_old} .
+        cp ~{cache_nextclade_old} .
         xz -T0 --decompress ~{basename(select_first([cache_nextclade_old,'']))}
         export NEXTCLADE_CACHE="~{basename(select_first([cache_nextclade_old,'']),'.xz')}"
       elif [[ $NEXTCLADE_CACHE == *.zst ]]; then
-        mv ~{cache_nextclade_old} .
+        cp ~{cache_nextclade_old} .
         zstd -T0 -d ~{basename(select_first([cache_nextclade_old]))}
         export NEXTCLADE_CACHE="~{basename(select_first([cache_nextclade_old,'']),'.zst')}"
       fi
 
-      mv $NEXTCLADE_CACHE ${NCOV_INGEST_DIR}/data/genbank/nextclade_old.tsv
+      cp $NEXTCLADE_CACHE ${NCOV_INGEST_DIR}/data/genbank/nextclade_old.tsv
       echo "nextclade_old.tsv has " `wc -l ${NCOV_INGEST_DIR}/data/genbank/nextclade_old.tsv` " records."
     fi