Merge pull request #35 from moka-guys/develop

v2.3.0 (#35) Co-Authored-By: Graeme <[email protected]>
moka-guys · Nov 9, 2023 · d28f8ba · d28f8ba
2 parents ad7a5b8 + e4f567b
commit d28f8ba
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Showing 2 changed files with 8 additions and 22 deletions.
diff --git a/config.py b/config.py
@@ -65,9 +65,9 @@
                 "regex": r"\S+_polyedge.pdf$",
             },
             "exomedepth": {
-                "folder":"/exomedepth_output", # TODO add
+                "folder": "/exomedepth_output",
                 "regex": r"\S+_output.pdf$",
-            }
+            },
         },
     ),
     "SNP": {
@@ -89,10 +89,6 @@
             "folder": "/QC",
             "regex": r"\S+_MergedSmallVariants.genome.vcf.stats.csv$",
         },
-        "results_zip": {
-            "folder": "/results",
-            "regex": r"\S+(?:{}).zip$",
-        },
         "metrics": {
             "folder": "/analysis_folder/Results/",
             "regex": r"^MetricsOutput\S*.tsv$",
@@ -165,16 +161,11 @@
                 "StG": False,
                 "subdir": r"sompy/",
             },
-            "results_zip": {
-                "Via": f"{P_BIOINF_TESTING}/TSO500/%s/",
-                "StG": False,
-                "subdir": r"Results/",
-            },
             "metrics": {
                 "Via": f"{P_BIOINF_TESTING}/TSO500/%s/",
                 "StG": False,
-                "subdir": r"Results/",
-        },
+                "subdir": r"metrics/",
+            },
         },
         **dict.fromkeys(["ArcherDX", "ONC"], False),
     },
@@ -239,16 +230,12 @@
                 "StG": False,
                 "subdir": r"sompy/",
             },
-            "results_zip": {
-                "Via": "S:/Genetics_Data2/TSO500/%s/",
-                "StG": False,
-                "subdir": r"Results/",
-            },
             "metrics": {
                 "Via": "S:/Genetics_Data2/TSO500/%s/",
                 "StG": False,
-                "subdir": r"Results/",
+                "subdir": r"metrics/",
+            },
+            **dict.fromkeys(["ArcherDX", "SWIFT"], False),
         },
-        **dict.fromkeys(["ArcherDX", "SWIFT"], False),
     },
-}}
+}
diff --git a/duty_csv.py b/duty_csv.py
@@ -642,7 +642,6 @@ def update_tso_config_regex(tso_pannumbers: list) -> None:
         for filetype in [
             "gene_level_coverage",
             "exon_level_coverage",
-            "results_zip",
         ]:
             config.PER_RUNTYPE_DOWNLOADS["TSO500"][filetype][
                 "regex"