Merge branch 'main' of github.com:ssi-dk/bifrost_sp_ecoli

bifrost_sp_ecoli/pipeline.smk

@@ -133,25 +133,24 @@ rule run_postecolityping:
         """
 
 
-# rule_name = "run_qc_ecoli_summary"
-# rule run_qc_ecoli_summary:
-#     message:
-#         f"Running step:{rule_name}"
-#     log:
-#         out_file = f"{component['name']}/log/{rule_name}.out.log",
-#         err_file = f"{component['name']}/log/{rule_name}.err.log",
-#     benchmark:
-#         f"{component['name']}/benchmarks/{rule_name}.benchmark",
-#     input:  # files
-#         rules.check_requirements.output.check_file,
-#     output:
-#         folder = directory(rules.setup.params.folder + "/ecoli_analysis"),
-#     shell:
-#         """
-#         # Summarize
-#         python3 ecoli_fbi/qc_ecoli_summary.py -i {output.folder} -o {output.folder} 1> {log.out_file} 2> {log.err_file}
-#         """
-
+rule_name = "run_qc_ecoli_summary"
+rule run_qc_ecoli_summary:
+    message:
+        f"Running step:{rule_name}"
+    log:
+        out_file = f"{component['name']}/log/{rule_name}.out.log",
+        err_file = f"{component['name']}/log/{rule_name}.err.log",
+    benchmark:
+        f"{component['name']}/benchmarks/{rule_name}.benchmark",
+    input:  # files
+        rules.check_requirements.output.check_file,
+    output:
+        folder = directory(rules.setup.params.folder + "/ecoli_analysis"),
+    shell:
+        """
+        # Summarize
+        python3 ecoli_fbi/qc_ecoli_summary.py -i {output.folder} -o {output.folder} 1> {log.out_file} 2> {log.err_file}
+        """
 
 #* Dynamic section: end ****************************************************************************
 

test/test_simple.py

@@ -0,0 +1,65 @@
+import os
+from pathlib import Path
+
+#import pymongo
+import pytest
+from bifrost_sp_ecoli import launcher
+from bifrostlib import common, database_interface, datahandling
+from bifrostlib.datahandling import (Component, ComponentReference, Run,
+                                     RunReference, Sample, SampleReference)
+
+
+bifrost_install_dir = os.environ['BIFROST_INSTALL_DIR']
+bifrost_config_and_data_path = Path(f"{bifrost_install_dir}/bifrost/test_data")
+
+@pytest.fixture
+def sample(use_collection):
+    json_entries = [
+        {
+            "_id": {"$oid": "000000000000000000000001"},
+            "display_name": "S1",
+            "name": "S1",
+            "components": [],
+            "categories": {
+                "paired_reads": {
+                    "summary": {
+                        "data": [f"{bifrost_config_and_data_path}/samples/S1_R1.fastq.gz",
+                                 f"{bifrost_config_and_data_path}/samples/S1_R2.fastq.gz"]
+                    }
+                }
+            }
+        }
+    ]
+    bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
+    use_collection("samples")
+    sample = Sample(value=json_entries[0])
+    sample.save()
+    return sample
+
+
+class TestBifrostSpEcoli:
+    component_name = "bifrost_sp_ecoli_v0.0.1"
+    current_dir = os.getcwd()
+    json_entries = [
+        {
+            "_id": {"$oid": "000000000000000000000001"},
+            "display_name": "S1",
+            "name": "S1",
+            "components": [],
+            "categories": {
+                "paired_reads": {
+                    "summary": {
+                        "data": [f"{bifrost_config_and_data_path}/samples/S1_R1.fastq.gz",
+                                 f"{bifrost_config_and_data_path}/samples/S1_R2.fastq.gz"]
+                    }
+                }
+            }
+        }
+    ]
+    bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
+
+    def test_info(self):
+        launcher.main(["launcher.py", "--info"])
+
+    def test_help(self):
+        launcher.main(["launcher.py", "--help"])