Fix file name for eukcc

The zip had a the internal cromwell path. This links and renames the file before zipping.
microbiomedata · Jul 2, 2024 · e13674c · e13674c
1 parent 582b976
commit e13674c
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/mbin_nmdc.wdl b/mbin_nmdc.wdl
@@ -409,6 +409,7 @@ task finish_mags {
         ln ~{heatmap} ~{prefix}_heatmap.pdf
         ln ~{kronaplot} ~{prefix}_kronaplot.html
         ln ~{ko_matrix} ~{prefix}_ko_matrix.txt
+        ln ~{eukcc_file} ~{prefix}_eukcc.csv
 
         # cp all tarfiles, zip them under prefix, if empty touch no_mags.txt
         mkdir -p hqmq
@@ -426,11 +427,11 @@ task finish_mags {
         if [ ~{n_lq} -gt 0 ] ; then
             (cd lq && cp ~{sep=" " lq_bin_tarfiles} .)
             (cd lq && cp ~{mbin_sdb} .)
-            (cd lq && zip -j ../~{prefix}_lq_bin.zip *tar.gz mbin.sdb ~{eukcc_file} ../*pdf ../*kronaplot.html ../*ko_matrix.txt)
+            (cd lq && zip -j ../~{prefix}_lq_bin.zip *tar.gz mbin.sdb ~{prefix}_eukcc.csv ../*pdf ../*kronaplot.html ../*ko_matrix.txt)
         else
             (cd lq && touch no_lq_mags.txt)
             (cd lq && cp ~{mbin_sdb} .)
-            (cd lq && zip ../~{prefix}_lq_bin.zip *.txt mbin.sdb ~{eukcc_file} )
+            (cd lq && zip ../~{prefix}_lq_bin.zip *.txt mbin.sdb ~{prefix}_eukcc.csv )
         fi
 
         # Fix up attribute name