Merge pull request #3 from sunbeam-labs/2-get-testing-working

Add dryrun test
sunbeam-labs · Feb 4, 2025 · abfa081 · abfa081
2 parents 4860cea + e4d0cdc
commit abfa081
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Showing 2 changed files with 41 additions and 11 deletions.
diff --git a/.tests/e2e/test_full_run.py → .tests/e2e/test_dry_run.py b/.tests/e2e/test_full_run.py → .tests/e2e/test_dry_run.py
@@ -18,7 +18,38 @@ def setup():
 
     config_fp = project_dir / "sunbeam_config.yml"
 
-    config_str = f"sbx_sga: {{example_rule_options: '--number'}}"
+    config_str = f"sbx_sga: {{mash_ref: '{temp_dir}/dummy.msh'}}"
+    Path(temp_dir / "dummy.msh").touch()
+
+    sp.check_output(
+        [
+            "sunbeam",
+            "config",
+            "modify",
+            "-i",
+            "-s",
+            f"{config_str}",
+            f"{config_fp}",
+        ]
+    )
+
+    config_str = f"sbx_sga: {{checkm_ref: '{temp_dir}/dummy.1.dmnd'}}"
+    Path(temp_dir / "dummy.1.dmnd").touch()
+
+    sp.check_output(
+        [
+            "sunbeam",
+            "config",
+            "modify",
+            "-i",
+            "-s",
+            f"{config_str}",
+            f"{config_fp}",
+        ]
+    )
+
+    config_str = f"sbx_sga: {{bakta_ref: '{temp_dir}/bakta/db/'}}"
+    Path(temp_dir / "bakta/db/").mkdir(parents=True, exist_ok=True)
 
     sp.check_output(
         [
@@ -52,29 +83,29 @@ def run_sunbeam(setup):
                 "run",
                 "--profile",
                 project_dir,
-                "all_template",
+                "all_sga",
                 "--directory",
                 temp_dir,
+                "-n",
             ]
         )
     except sp.CalledProcessError as e:
         shutil.copytree(log_fp, "logs/")
         shutil.copytree(stats_fp, "stats/")
         sys.exit(e)
 
-    shutil.copytree(log_fp, "logs/")
-    shutil.copytree(stats_fp, "stats/")
+    # shutil.copytree(log_fp, "logs/")
+    # shutil.copytree(stats_fp, "stats/")
+    Path("logs/").mkdir(parents=True, exist_ok=True)
+    Path("stats/").mkdir(parents=True, exist_ok=True)
+    Path("logs/file").touch()
+    Path("stats/file").touch()
 
     output_fp = project_dir / "sunbeam_output"
     benchmarks_fp = project_dir / "stats/"
 
     yield output_fp, benchmarks_fp
 
 
-def test_full_run(run_sunbeam):
+def test_dry_run(run_sunbeam):
     output_fp, benchmarks_fp = run_sunbeam
-
-    big_file_fp = output_fp / "qc/mush/big_file.txt"
-
-    # Check output
-    assert big_file_fp.exists(), f"{big_file_fp} does not exist"
diff --git a/sbx_sga.smk b/sbx_sga.smk
@@ -27,7 +27,6 @@ localrules:
 rule all_sga:
     input:
         # QC
-        #expand(ISOLATE_FP / "fastqc" / "{sample}_{rp}_fastqc/fastqc_data.txt", rp=Pairs, sample=Samples),
         expand(ISOLATE_FP / "mash" / "{sample}_sorted_winning.tab", sample=Samples),
         # Assembly QC
         ISOLATE_FP / "checkm" / "quality_report.tsv",