Fixed the test to pass. Still need to test the actual report.

EdinburghGenomics · Feb 26, 2024 · 378c5eb · 378c5eb
1 parent 6f5dbe0
commit 378c5eb
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/test/examples/runs/20221103_EGS2_25070AT/sc_data.yaml b/test/examples/runs/20221103_EGS2_25070AT/sc_data.yaml
@@ -268,6 +268,11 @@ representative_pod5:
   25070AT0003/20221104_1306_1G_PAM78534_6623d643: null
   25070AT0004/20221103_1710_1D_PAM83454_1f1b14bd: null
   25070AT0005/20221103_1710_1B_PAM82832_3ed26d0e: null
+representative_fastq:
+  25070AT0003/20221103_1710_1F_PAM83464_136e9f68: 25070AT0003/20221103_1710_1F_PAM83464_136e9f68/20221103_EGS2_25070AT_25070AT0003_PAM83464_136e9f68_barcode01_pass.fastq.gz
+  25070AT0003/20221104_1306_1G_PAM78534_6623d643: 25070AT0003/20221104_1306_1G_PAM78534_6623d643/20221103_EGS2_25070AT_25070AT0003_PAM78534_6623d643_barcode01_pass.fastq.gz
+  25070AT0004/20221103_1710_1D_PAM83454_1f1b14bd: 25070AT0004/20221103_1710_1D_PAM83454_1f1b14bd/20221103_EGS2_25070AT_25070AT0004_PAM83454_1f1b14bd_barcode01_pass.fastq.gz
+  25070AT0005/20221103_1710_1B_PAM82832_3ed26d0e: 25070AT0005/20221103_1710_1B_PAM82832_3ed26d0e/20221103_EGS2_25070AT_25070AT0005_PAM82832_3ed26d0e_barcode01_pass.fastq.gz
 scanned_cells:
   25070AT0003/20221103_1710_1F_PAM83464_136e9f68:
     barcode01:

diff --git a/test/examples/runs/20231107_MIN2_26171SS/sc_data.yaml b/test/examples/runs/20231107_MIN2_26171SS/sc_data.yaml
@@ -24,6 +24,8 @@ representative_fast5:
   26171SS0001L02/20231108_1411_MN32284_AOZ898_35873099: null
 representative_pod5:
   26171SS0001L02/20231108_1411_MN32284_AOZ898_35873099: 26171SS0001L02/20231108_1411_MN32284_AOZ898_35873099/pod5_._pass/AOZ898_pass_35873099_e8dfad65_batch100_00000000.pod5
+representative_fastq:
+  26171SS0001L02/20231108_1411_MN32284_AOZ898_35873099: 26171SS0001L02/20231108_1411_MN32284_AOZ898_35873099/foobarfoo_26171SS0001L02_AOZ898_35873099_._pass.fastq.gz
 scanned_cells:
   26171SS0001L02/20231108_1411_MN32284_AOZ898_35873099:
     .:

diff --git a/test/test_scan_cells.py b/test/test_scan_cells.py
@@ -71,7 +71,7 @@ def test_scan_main(self):
             on the command line.
         """
         args = parse_args([f"{DATA_DIR}/runs/20221103_EGS2_25070AT"])
-        sc = scan_main( args )
+        sc = scan_main( args, "20221103_EGS2_25070AT" )
 
         with open(f"{DATA_DIR}/runs/20221103_EGS2_25070AT/sc_data.yaml") as yfh:
             expected = yaml.safe_load(yfh)
@@ -87,7 +87,7 @@ def test_scan_main_pod5(self):
         """ A test using the run I was using to test pod5 runs.
         """
         args = parse_args([f"{DATA_DIR}/runs/20231107_MIN2_26171SS"])
-        sc = scan_main( args )
+        sc = scan_main( args, "foobarfoo" )
 
         with open(f"{DATA_DIR}/runs/20231107_MIN2_26171SS/sc_data.yaml") as yfh:
             expected = yaml.safe_load(yfh)