fix: allow zero subtractions in nuvs

.gitignore

@@ -2,3 +2,4 @@ __pycache__
 .idea
 .pytest_cache
 /target/
+.vscode

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

tests/test_workflow.py

@@ -26,6 +26,7 @@
 from virtool_workflow.data_model.indexes import WFIndex
 from virtool_workflow.data_model.samples import WFSample
 from virtool_workflow.data_model.subtractions import WFSubtraction
+from virtool_workflow.runtime.run_subprocess import RunSubprocess
 
 from workflow import (
     eliminate_otus,
@@ -227,13 +228,32 @@ async def test_eliminate_otus(
     assert actual == expected
 
 
+@pytest.mark.parametrize("no_subtractions", [True, False])
 async def test_eliminate_subtraction(
-    run_subprocess, subtractions: list[WFSubtraction], work_path: Path
+    no_subtractions: bool,
+    run_subprocess: RunSubprocess,
+    subtractions: list[WFSubtraction],
+    work_path,
 ):
+    if no_subtractions:
+        subtractions = []
+
     shutil.copy(TEST_DATA_PATH / "unmapped_otus.fq", work_path / "unmapped_otus.fq")
     await eliminate_subtraction(2, run_subprocess, subtractions, work_path)
 
+    assert Path(work_path / "unmapped_subtraction.fq").is_file()
+
+    if no_subtractions:
+        with open(work_path / "unmapped_subtraction.fq") as subtracted_file, open(
+            work_path / "unmapped_otus.fq"
+        ) as otu_file:
+            subtracted_lines = [line.strip() for line in subtracted_file]
+            otu_lines = [line.strip() for line in otu_file]
+            for subtracted, otu in zip(subtracted_lines, otu_lines):
+                assert subtracted == otu
+
 
+@pytest.mark.flaky(reruns=3)
 @pytest.mark.parametrize("paired", [False, True], ids=["unpaired", "paired"])
 async def test_reunite_pairs(paired: bool, reads: Reads, sample: WFSample, work_path):
     if paired:

workflow.py

@@ -88,7 +88,11 @@ async def eliminate_subtraction(
     """
 
     if len(subtractions) == 0:
-        return
+        await asyncio.to_thread(
+            shutil.copyfile,
+            work_path / "unmapped_otus.fq",
+            work_path / "unmapped_subtraction.fq",
+        )
 
     await asyncio.to_thread(
         shutil.copyfile, work_path / "unmapped_otus.fq", work_path / "working_otus.fq"
@@ -105,7 +109,7 @@ async def eliminate_subtraction(
             "-x",
             shlex.quote(str(subtraction.bowtie2_index_path)),
             "--un",
-            str(work_path / "unmapped_subtractions.fq"),
+            str(work_path / "unmapped_subtraction.fq"),
             "-U",
             str(work_path / "working_otus.fq"),
         ]
@@ -114,7 +118,7 @@ async def eliminate_subtraction(
 
         await asyncio.to_thread(
             shutil.copyfile,
-            work_path / "unmapped_subtractions.fq",
+            work_path / "unmapped_subtraction.fq",
             work_path / "working_otus.fq",
         )