Fix the unstable api of snakemake to work again

Removing a command line flag, and also switching error output again to stderr.

tests/functional/simple_snakefile_test_cases.yml

@@ -1,26 +1,26 @@
 - name: test-dry-run
-  command: snakemake -n -r -p -s SimpleSnakefile --config N_LINES_TO_READ=1
+  command: snakemake -n -p -s SimpleSnakefile --config N_LINES_TO_READ=1
 - name: test-config-missing
-  command: snakemake -n -r -p -s SimpleSnakefile
+  command: snakemake -n -p -s SimpleSnakefile
   exit_code: 1
-  stdout:
+  stderr:
     contains:
       - "You must set --config N_LINES_TO_READ=<a value>."
 - name: test-config-wrong-type
-  command: snakemake -n -r -p -s SimpleSnakefile --config N_LINES_TO_READ=one
+  command: snakemake -n -p -s SimpleSnakefile --config N_LINES_TO_READ=one
   exit_code: 1
-  stdout:
+  stderr:
     contains:
       - "N_LINES_TO_READ must be an integer."
 - name: test-config-invalid-value
-  command: snakemake -n -r -p -s SimpleSnakefile --config N_LINES_TO_READ=-1
+  command: snakemake -n -p -s SimpleSnakefile --config N_LINES_TO_READ=-1
   exit_code: 1
-  stdout:
+  stderr:
     contains:
       - "N_LINES_TO_READ must at least be 1."
 - name: test-snakemake-run
   command: >-
-    snakemake --cores 1 -r -p -s SimpleSnakefile --config N_LINES_TO_READ=500
+    snakemake --cores 1 -p -s SimpleSnakefile --config N_LINES_TO_READ=500
   files:
     - path: rand/0.txt
     - path: rand/1.txt