add ngi_data dir, clarify test scope

SciLifeLab · Apr 10, 2024 · 3b317ba · 3b317ba
1 parent 47cb0ab
commit 3b317ba
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Showing 3 changed files with 49 additions and 49 deletions.
diff --git a/tests/analysis/test_analysis.py b/tests/analysis/test_analysis.py
@@ -376,21 +376,22 @@ def create_illumina_run_dir(
     e.g.
 
         tmp
-        └── sequencing
-            └── NovaSeqXPlus
-                └── 20240202_LH00217_0044_A2255J2LT3
-                    ├── CopyComplete.txt
-                    ├── Demultiplexing
-                    ├── RTAComplete.txt
-                    ├── RunInfo.xml
-                    ├── RunParameters.xml
-                    └── SampleSheet.csv
+        └── ngi_data
+            └── sequencing
+                └── NovaSeqXPlus
+                    └── 20240202_LH00217_0044_A2255J2LT3
+                        ├── CopyComplete.txt
+                        ├── Demultiplexing
+                        ├── RTAComplete.txt
+                        ├── RunInfo.xml
+                        ├── RunParameters.xml
+                        └── SampleSheet.csv
 
     Return it's path.
     """
 
     # Get run path
-    run_path = f"{tmp.name}/sequencing/{instrument}/{run_name}"
+    run_path = f"{tmp.name}/ngi_data/sequencing/{instrument}/{run_name}"
 
     # Create runs directory structure
     if os.path.exists(run_path):
@@ -549,7 +550,7 @@ def create_illumina_run_dir(
     return run_path
 
 
-def test_get_runObj(create_dirs):
+def test_run_preprocessing(create_dirs):
     tmp = create_dirs
 
     # Mock CONFIG
@@ -577,7 +578,7 @@ def test_get_runObj(create_dirs):
             level = test_config_yaml.get("log").get("log_level", "INFO")
             init_logger_file(log_file, level)
 
-        # Start demux
-        analysis.run_preprocessing(run_path, software)
-        # Demux in progress
+        # Start demux, all runs
+        analysis.run_preprocessing(None, software)
+        # Demux in progress, specified run
         analysis.run_preprocessing(run_path, software)
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -34,46 +34,45 @@ def create_dirs():
         │   └── samplesheets
         │       ├── NovaSeqXPlus
         │       └── anglerfish
-        └── sequencing
-            ├── MiSeq
-            │   └── nosync
-            ├── NextSeq
-            │   └── nosync
-            ├── NovaSeq
-            │   └── nosync
-            ├── NovaSeqXPlus
-            │   └── nosync
-            ├── minion
-            │   ├── nosync
-            │   └── qc
-            │       └── nosync
-            └── promethion
-                └── nosync
+        └── ngi_data
+            └── sequencing
+                ├── MiSeq
+                │   └── nosync
+                ├── NextSeq
+                │   └── nosync
+                ├── NovaSeq
+                │   └── nosync
+                ├── NovaSeqXPlus
+                │   └── nosync
+                ├── minion
+                │   ├── nosync
+                │   └── qc
+                │       └── nosync
+                └── promethion
+                    └── nosync
 
     --> Return the the temporary directory object
     """
     tmp = tempfile.TemporaryDirectory()
 
-    # CREATE DIR STRUCTURE
-
     # Sequencing data
-    # Illumina
-    os.makedirs(f"{tmp.name}/sequencing/MiSeq/nosync")
-    os.makedirs(f"{tmp.name}/sequencing/NextSeq/nosync")
-    os.makedirs(f"{tmp.name}/sequencing/NovaSeq/nosync")
-    os.makedirs(f"{tmp.name}/sequencing/NovaSeqXPlus/nosync")
-    # ONT
-    os.makedirs(f"{tmp.name}/sequencing/promethion/nosync")
-    os.makedirs(f"{tmp.name}/sequencing/minion/nosync")
-    os.makedirs(f"{tmp.name}/sequencing/minion/qc/nosync")
+    ## Illumina
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/MiSeq/nosync")
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/NextSeq/nosync")
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/NovaSeq/nosync")
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/NovaSeqXPlus/nosync")
+    ## ONT
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/promethion/nosync")
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/minion/nosync")
+    os.makedirs(f"{tmp.name}/ngi_data/sequencing/minion/qc/nosync")
 
     # Sequencing metadata
-    # Illumina
+    ## Illumina
     os.makedirs(f"{tmp.name}/ngi-nas-ns/miseq_data")
     os.makedirs(f"{tmp.name}/ngi-nas-ns/NextSeq_data")
     os.makedirs(f"{tmp.name}/ngi-nas-ns/NovaSeq_data")
     os.makedirs(f"{tmp.name}/ngi-nas-ns/NovaSeqXPlus_data")
-    # ONT
+    ## ONT
     os.makedirs(f"{tmp.name}/ngi-nas-ns/promethion_data")
     os.makedirs(f"{tmp.name}/ngi-nas-ns/minion_data")
 

diff --git a/tests/nanopore/test_ONT_run_classes.py b/tests/nanopore/test_ONT_run_classes.py
@@ -19,31 +19,31 @@ def make_ONT_test_config(tmp: tempfile.TemporaryDirectory) -> dict:
     run_types:
         user_run:
             data_dirs:
-                - {tmp.name}/sequencing/promethion
-                - {tmp.name}/sequencing/minion
+                - {tmp.name}/ngi_data/sequencing/promethion
+                - {tmp.name}/ngi_data/sequencing/minion
             ignore_dirs:
                 - 'nosync'
                 - 'qc'
             instruments:
                 promethion:
                     transfer_log: {tmp.name}/log/transfer_promethion.tsv
-                    archive_dir: {tmp.name}/sequencing/promethion/nosync
+                    archive_dir: {tmp.name}/ngi_data/sequencing/promethion/nosync
                     metadata_dir: {tmp.name}/ngi-nas-ns/promethion_data
                     destination: {tmp.name}/miarka/promethion/
                 minion:
                     transfer_log: {tmp.name}/log/transfer_minion.tsv
-                    archive_dir: {tmp.name}/sequencing/minion/nosync
+                    archive_dir: {tmp.name}/ngi_data/sequencing/minion/nosync
                     metadata_dir: {tmp.name}/ngi-nas-ns/minion_data
                     destination: {tmp.name}/miarka/minion/
         qc_run:
             data_dirs:
-                - {tmp.name}/sequencing/minion/qc
+                - {tmp.name}/ngi_data/sequencing/minion/qc
             ignore_dirs:
                 - 'nosync'
             instruments:
                 minion:
                     transfer_log: {tmp.name}/log/transfer_minion_qc.tsv
-                    archive_dir: {tmp.name}/sequencing/minion/qc/nosync
+                    archive_dir: {tmp.name}/ngi_data/sequencing/minion/qc/nosync
                     metadata_dir: {tmp.name}/ngi-nas-ns/minion_data/qc
                     destination: {tmp.name}/miarka/minion/qc
             anglerfish:
@@ -118,7 +118,7 @@ def create_ONT_run_dir(
         instrument = "minion"
         instrument_position = "MN19414"
     if not data_dir:
-        data_dir = f"{tmp.name}/sequencing/{instrument}"
+        data_dir = f"{tmp.name}/ngi_data/sequencing/{instrument}"
 
     run_name = f"{run_start_time}_{instrument_position}_{flowcell_id}_{run_id}"
     if qc: