Merge branch '85_amrfinderplusannotation_type' into 87_annotate_mags_…

…amrfinderplus
bokulich-lab · Jul 10, 2024 · 81f0fbb · 81f0fbb
2 parents f10dcb3 + bbaca6e
commit 81f0fbb
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/q2_amr/amrfinderplus/types/_format.py b/q2_amr/amrfinderplus/types/_format.py
@@ -115,12 +115,13 @@ def _validate_(self, level):
 
 class ARMFinderPlusAnnotationsDirFmt(MultiDirValidationMixin, model.DirectoryFormat):
     annotation = model.FileCollection(
-        r".+_amr_(annotations|mutations)\.tsv$", format=ARMFinderPlusAnnotationFormat
+        r".+amr_(annotations|mutations)\.tsv$", format=ARMFinderPlusAnnotationFormat
     )
 
     @annotation.set_path_maker
     def annotation_path_maker(self, sample_id, mag_id):
-        return rf"{sample_id}/{mag_id}_amr_(annotations|mutations)\.tsv$"
+        prefix = f"{sample_id}/{mag_id}_" if mag_id else f"{sample_id}/"
+        return f"{prefix}amr_annotations.tsv"
 
 
 ARMFinderPlusAnnotationDirFmt = model.SingleFileDirectoryFormat(