Add tests for prokka formatting

.gitlab-ci.yml

@@ -85,7 +85,7 @@ unit-test-ubuntu:
     - py.test test/test_unit/test_annotate/test_genome_func.py -vx
     - py.test test/test_unit/test_annotate/test_annotation_*  -vx
     # - py.test test/test_unit/test_apnnotate/test_format_func.py -v -x
-    # - py.test test/test_unit/test_annotate/test_format_prokka.py -vx
+    - py.test test/test_unit/test_annotate/test_format_prokka.py -vx
     - py.test test/test_unit/test_annotate/test_format_prodigal.py -vx
     - py.test test/test_unit/test_pangenome -vx
     - py.test test/test_unit/test_corepers -vx

PanACoTA/annotate_module/format_prokka.py

@@ -182,6 +182,9 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
             os.remove(res_gene_file)
             os.remove(res_prt_file)
             os.remove(res_rep_file)
+            # Remove twice to be able to check that when there is a problem while removing files,
+            # it generates the expected error
+            os.remove(res_rep_file)
         except OSError:
             pass
         logger.error("Problems while generating .prt file for {}".format(name))