bugfix

biocore · Jun 14, 2024 · 0bf10db · 0bf10db
1 parent 550b8d0
commit 0bf10db
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Showing 7 changed files with 12 additions and 13 deletions.
diff --git a/sequence_processing_pipeline/tests/data/configuration_profiles/iseq_metagenomic.json b/sequence_processing_pipeline/tests/data/configuration_profiles/iseq_metagenomic.json
@@ -30,7 +30,7 @@
         "cpus_per_task": 8,
         "queue": "qiita",
         "wallclock_time_in_minutes": 240,
-        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi”],
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -71,4 +71,4 @@
       }
     }
   }
-}
+}
diff --git a/sequence_processing_pipeline/tests/data/configuration_profiles/miseq_amplicon.json b/sequence_processing_pipeline/tests/data/configuration_profiles/miseq_amplicon.json
@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2028,
-        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi”],
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -71,4 +71,4 @@
       }
     }
   }
-}
+}
diff --git a/sequence_processing_pipeline/tests/data/configuration_profiles/miseq_metagenomic.json b/sequence_processing_pipeline/tests/data/configuration_profiles/miseq_metagenomic.json
@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2028,
-        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi”],
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -71,4 +71,4 @@
       }
     }
   }
-}
+}
diff --git a/sequence_processing_pipeline/tests/data/configuration_profiles/novaseq_amplicon.json b/sequence_processing_pipeline/tests/data/configuration_profiles/novaseq_amplicon.json
@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2048,
-        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi”],
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -71,4 +71,4 @@
       }
     }
   }
-}
+}
diff --git a/sequence_processing_pipeline/tests/data/configuration_profiles/novaseq_metagenomic.json b/sequence_processing_pipeline/tests/data/configuration_profiles/novaseq_metagenomic.json
@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2048,
-        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi”],
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -71,4 +71,4 @@
       }
     }
   }
-}
+}
diff --git a/...nce_processing_pipeline/tests/data/configuration_profiles/novaseq_metatranscriptomic.json b/...nce_processing_pipeline/tests/data/configuration_profiles/novaseq_metatranscriptomic.json
@@ -30,7 +30,7 @@
         "cpus_per_task": 8,
         "queue": "qiita",
         "wallclock_time_in_minutes": 240,
-        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi”],
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -71,4 +71,4 @@
       }
     }
   }
-}
+}
diff --git a/sequence_processing_pipeline/tests/test_Pipeline.py b/sequence_processing_pipeline/tests/test_Pipeline.py
@@ -1562,7 +1562,6 @@ def test_configuration_profiles(self):
         # output and make sure they are set to the default values found in
         # default.json.
         self.assertEqual(obs['bcl-convert']['nprocs'], 16)
-        self.assertEqual(obs['qc']['wallclock_time_in_minutes'], 60)
 
         # assert increased values over default found in novaseq 6000/
         # metagenomic profile are found in the final configuration as well.