Merge pull request #156 from charles-cowart/fastq_description_update

Update to optional description support
biocore · Oct 21, 2024 · 867ad4d · 867ad4d
2 parents 9d5b7d4 + 49c773d
commit 867ad4d
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Showing 2 changed files with 47 additions and 3 deletions.
diff --git a/sequence_processing_pipeline/NuQCJob.py b/sequence_processing_pipeline/NuQCJob.py
@@ -410,8 +410,10 @@ def _generate_mmi_filter_cmds(self, working_dir):
             # been annotated with. Samtools will safely ignore tags that
             # are not present.
             tags = " -T %s" % ','.join(self.additional_fastq_tags)
+            t_switch = " -y"
         else:
             tags = ""
+            t_switch = ""
 
         for count, mmi_db_path in enumerate(self.mmi_file_paths):
             if count == 0:
@@ -428,7 +430,7 @@ def _generate_mmi_filter_cmds(self, working_dir):
                 input = tmp_file1
                 output = tmp_file2
 
-            cmds.append(f"minimap2 -2 -ax sr -y -t {cores_to_allocate} "
+            cmds.append(f"minimap2 -2 -ax sr{t_switch} -t {cores_to_allocate} "
                         f"{mmi_db_path} {input} -a | samtools fastq -@ "
                         f"{cores_to_allocate} -f 12 -F 256{tags} > "
                         f"{output}")

diff --git a/sequence_processing_pipeline/tests/test_NuQCJob.py b/sequence_processing_pipeline/tests/test_NuQCJob.py
@@ -2108,10 +2108,10 @@ def test_generate_mmi_filter_cmds(self):
         obs = job._generate_mmi_filter_cmds("/my_work_dir")
 
         exp = [
-            "minimap2 -2 -ax sr -y -t 2 db_path/mmi_1.db /my_work_dir/seqs."
+            "minimap2 -2 -ax sr -t 2 db_path/mmi_1.db /my_work_dir/seqs."
             "interleaved.fastq -a | samtools fastq -@ 2 -f 12 -F 256 > "
             "/my_work_dir/foo",
-            "minimap2 -2 -ax sr -y -t 2 db_path/mmi_2.db /my_work_dir/foo -a"
+            "minimap2 -2 -ax sr -t 2 db_path/mmi_2.db /my_work_dir/foo -a"
             " | samtools fastq -@ 2 -f 12 -F 256 > /my_work_dir/bar",
             "mv /my_work_dir/bar /my_work_dir/seqs.interleaved.filter_"
             "alignment.fastq",
@@ -2123,6 +2123,48 @@ def test_generate_mmi_filter_cmds(self):
 
         self.assertEqual(obs, exp)
 
+    def test_generate_mmi_filter_cmds_w_descriptions(self):
+        double_db_paths = ["db_path/mmi_1.db", "db_path/mmi_2.db"]
+        job = NuQCJob(
+            self.fastq_root_path,
+            self.output_path,
+            self.good_sample_sheet_path,
+            double_db_paths,
+            "queue_name",
+            1,
+            1440,
+            "8",
+            "fastp",
+            "minimap2",
+            "samtools",
+            [],
+            self.qiita_job_id,
+            1000,
+            "",
+            self.movi_path,
+            self.gres_value,
+            self.pmls_path,
+            ["BX"]
+        )
+
+        obs = job._generate_mmi_filter_cmds("/my_work_dir")
+
+        exp = [
+            "minimap2 -2 -ax sr -y -t 2 db_path/mmi_1.db /my_work_dir/seqs."
+            "interleaved.fastq -a | samtools fastq -@ 2 -f 12 -F 256 -T BX > "
+            "/my_work_dir/foo",
+            "minimap2 -2 -ax sr -y -t 2 db_path/mmi_2.db /my_work_dir/foo -a"
+            " | samtools fastq -@ 2 -f 12 -F 256 -T BX > /my_work_dir/bar",
+            "mv /my_work_dir/bar /my_work_dir/seqs.interleaved.filter_"
+            "alignment.fastq",
+            "[ -e /my_work_dir/foo ] && rm /my_work_dir/foo",
+            "[ -e /my_work_dir/bar ] && rm /my_work_dir/bar",
+        ]
+
+        exp = "\n".join(exp)
+
+        self.assertEqual(obs, exp)
+
     def test_generate_mmi_filter_cmds_w_annotate_fastq(self):
         double_db_paths = ["db_path/mmi_1.db", "db_path/mmi_2.db"]
         job = NuQCJob(