fix: actually fix the bug that disabled stitching (#7)

Had input xml used instead of output xml, which was causing the
stitching transform to be applied to the bdv xml instead of the actual
output xml (since it writes in-place)..

workflow/rules/common.smk

@@ -128,7 +128,7 @@ def get_fiji_launcher_cmd(wildcards, output, threads, resources):
 
 def get_macro_args_bigstitcher(wildcards, input, output):
     return "{dataset_xml} {ds_x} {ds_y} {ds_z} {min_r}".format(
-        dataset_xml=input.dataset_xml,
+        dataset_xml=output.dataset_xml,
         ds_x=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_x"],
         ds_y=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_y"],
         ds_z=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_z"],