fix tests

nextstrain · Feb 11, 2025 · b0799eb · b0799eb
1 parent 398f972
commit b0799eb
Showing 1 changed file with 6 additions and 7 deletions.
diff --git a/tests/functional/tree/cram/iqtree-offending-characters.t b/tests/functional/tree/cram/iqtree-offending-characters.t
@@ -8,12 +8,11 @@ Build a tree with offending characters, and ensure characters are not overwritte
   >  --alignment "$TESTDIR/../data/aligned_offending_characters.fasta" \
   >  --method iqtree \
   >  --output tree_raw.nwk \
-  >  --nthreads 1 > /dev/null
-  "WARNING: Potentially offending character ''' detected in taxon name KX369547.1/Cote_d'Ivore. We recommend replacing offending characters with '_' in the alignment file to avoid issues downstream."
-  [1]
+  >  --nthreads 1 | head -n 1
+  WARNING: Potentially offending character "'" detected in taxon name "KX369547.1/Cote_d'Ivore".  We recommend replacing offending characters with '_' in the alignment file to avoid issues downstream.
 
-  $ cat "$TESTDIR/tree_raw.nwk" | grep -q "Cote_d'Ivore" && echo "Substring found"
-    Substring found
+  $ cat "tree_raw.nwk" | grep -q "Cote_d'Ivore" && echo "Substring found"
+  Substring found
 
-  $ cat "$TESTDIR/tree_raw.nwk" | grep -q "United-Arab-Emirates" && echo "Substring found"
-    Substring found
+  $ cat "tree_raw.nwk" | grep -q "United-Arab-Emirates" && echo "Substring found"
+  Substring found