Fix #432 annotate can fail with 'Failed to instantiate plugin GADO' (#…

…434) * Fix #432 annotate can fail with 'Failed to instantiate plugin GADO' * fix
molgenis · Jul 24, 2023 · 816e78d · 816e78d
1 parent e952784
commit 816e78d
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/modules/vcf/templates/annotate.sh b/modules/vcf/templates/annotate.sh
@@ -80,6 +80,12 @@ gado_prioritize() {
   args+=("--hpoPredictions" "!{gadoPredictMatrixPath}")
 
   ${CMD_GADO} java "${args[@]}"
+
+  # workaround for GADO sometimes not producing a all_samples.txt after successfull exit
+  # https://github.com/molgenis/systemsgenetics/issues/663
+  if [[ ! -f "./gado/all_samples.txt" ]]; then
+    echo -e "Ensg\tHgnc\tRank\tZscore\t$(sed "s/,/\t/g" <<< "!{gadoHpoIds}")" > "./gado/all_samples.txt"
+  fi
 }
 
 capice() {