Merge branch 'trs/merge/tests'

tests/functional/merge/cram/merge.t

@@ -1,6 +1,7 @@
 SETUP
 
   $ export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+  $ set -o pipefail
 
 
 BASIC USAGE
@@ -183,29 +184,6 @@ Metadata field values with metachars (field or record delimiters) are handled pr
   x"	1	1
   two	X2a	X2b	X2c				1	1
 
-Output column renamed when it conflicts with id column.
-
-  $ cat >id-and-strain.csv <<~~
-  > id,strain
-  > one,1
-  > two,2
-  > three,3
-  > ~~
-  $ ${AUGUR} merge \
-  >   --metadata strain-only=x.tsv id-and-strain=id-and-strain.csv \
-  >   --metadata-id-columns id strain \
-  >   --output-metadata - | csv2tsv --csv-delim $'\t' | tsv-pretty
-  ERROR: Non-id column names in metadata inputs may not conflict with the
-  output id column name ('strain', the first input's id column).
-
-  The following input column would conflict:
-
-    'strain' in metadata table 'id-and-strain' (id column: 'id')
-
-  Please rename or drop the conflicting column before merging.
-  Renaming may be done with `augur curate rename`.
-
-
 
 ERROR HANDLING
 
@@ -323,6 +301,30 @@ No id column found.
   ERROR: x-id-column.tsv: None of the possible id columns ('strain') were found in the metadata's columns ('id', 'a', 'b', 'c').
   [2]
 
+Non-id column names conflicting with output id column name.
+
+  $ cat >id-and-strain.csv <<~~
+  > id,strain
+  > one,1
+  > two,2
+  > three,3
+  > ~~
+  $ ${AUGUR} merge \
+  >   --metadata strain-only=x.tsv id-and-strain=id-and-strain.csv \
+  >   --metadata-id-columns id strain \
+  >   --output-metadata /dev/null --quiet
+  ERROR: Non-id column names in metadata inputs may not conflict with the
+  output id column name ('strain', the first input's id column).
+
+  The following input column would conflict:
+
+    'strain' in metadata table 'id-and-strain' (id column: 'id')
+
+  Please rename or drop the conflicting column before merging.
+  Renaming may be done with `augur curate rename`.
+
+  [2]
+
 SQLITE3 env var can be used to override `sqlite3` location (and failure is
 handled).