fix: add batch test to test integration

test/example_batch.tsv → test/data/example_batch.tsv

@@ -1,3 +1,3 @@
 sample short_reads_1 short_reads_2 long_reads long_read_type assembly coassemble
 sample_1 test/data/wgsim.1.fq.gz test/data/wgsim.2.fq.gz NA ont NA NA
-sample_2 NA NA test/data/pbsim.fq.gz pacbio NA NA
+sample_2 test/data/wgsim.1.fq.gz test/data/wgsim.2.fq.gz test/data/pbsim.fq.gz ont NA NA

test/test_integration.py

@@ -162,7 +162,6 @@ def test_short_read_recovery_queue_submission(self):
 
         cmd = (
             f"aviary recover "
-            f"--output {output_dir} "
             f"-o {output_dir}/aviary_out "
             f"-1 {data}/wgsim.1.fq.gz "
             f"-2 {data}/wgsim.2.fq.gz "
@@ -180,6 +179,41 @@ def test_short_read_recovery_queue_submission(self):
             num_lines = sum(1 for _ in f)
         self.assertEqual(num_lines, 3)
 
+    def test_batch_recovery(self):
+        output_dir = os.path.join("example", "test_batch_recovery")
+        self.setup_output_dir(output_dir)
+        cmd = (
+            f"aviary batch "
+            f"-o {output_dir}/aviary_out "
+            f"-f {data}/example_batch.tsv "
+            f"--conda-prefix {path_to_conda} "
+            f"--skip-binners rosella vamb metabat "
+            f"--skip-qc "
+            f"--refinery-max-iterations 0 "
+            f"--min-read-size 10 --min-mean-q 1 "
+            f"-n 32 -t 32 "
+        )
+        subprocess.run(cmd, shell=True, check=True)
+
+        self.assertTrue(os.path.isfile(f"{output_dir}/aviary_out/sample_1/data/final_contigs.fasta"))
+        self.assertTrue(os.path.isfile(f"{output_dir}/aviary_out/sample_2/data/final_contigs.fasta"))
+
+        bin_info_path_1 = f"{output_dir}/aviary_out/sample_1/bins/bin_info.tsv"
+        bin_info_path_2 = f"{output_dir}/aviary_out/sample_2/bins/bin_info.tsv"
+        self.assertTrue(os.path.isfile(bin_info_path_1))
+        self.assertTrue(os.path.isfile(bin_info_path_2))
+        with open(bin_info_path_1) as f:
+            num_lines = sum(1 for _ in f)
+        self.assertEqual(num_lines, 3)
+
+        self.assertTrue(os.path.isdir(f"{output_dir}/aviary_out/aviary_cluster_ani_0.95"))
+        self.assertTrue(os.path.isdir(f"{output_dir}/aviary_out/aviary_cluster_ani_0.97"))
+        self.assertTrue(os.path.isdir(f"{output_dir}/aviary_out/aviary_cluster_ani_0.99"))
+
+        self.assertTrue(os.path.isdir(f"{output_dir}/aviary_out/aviary_cluster_ani_0.95/pangenomes"))
+        self.assertTrue(os.path.isdir(f"{output_dir}/aviary_out/aviary_cluster_ani_0.97/pangenomes"))
+        self.assertTrue(os.path.isdir(f"{output_dir}/aviary_out/aviary_cluster_ani_0.99/pangenomes"))
+
 
 if __name__ == "__main__":
     unittest.main()