From c65e52644899b2e1b1308af79c4193eb3fdf1ae7 Mon Sep 17 00:00:00 2001
From: Rachel Duffin <rachel.g.duffin@gmail.com>
Date: Tue, 7 Nov 2023 10:57:23 +0000
Subject: [PATCH 1/2] Remove TSO zip file download (replaced by qiagen_upload)

---
 config.py   | 14 --------------
 duty_csv.py |  1 -
 2 files changed, 15 deletions(-)

diff --git a/config.py b/config.py
index 68c0bca..c6babfc 100644
--- a/config.py
+++ b/config.py
@@ -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$",
@@ -165,11 +161,6 @@
                 "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,
@@ -239,11 +230,6 @@
                 "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,
diff --git a/duty_csv.py b/duty_csv.py
index 6437df8..729a6a4 100644
--- 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"

From b4c8e6c666ae44b18c5c53d8959cd0131bff66ae Mon Sep 17 00:00:00 2001
From: Rachel Duffin <rachel.g.duffin@gmail.com>
Date: Tue, 7 Nov 2023 15:43:19 +0000
Subject: [PATCH 2/2] Update output location of metrics files on trust network

---
 config.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/config.py b/config.py
index c6babfc..33ce3e3 100644
--- 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": {
@@ -164,8 +164,8 @@
             "metrics": {
                 "Via": f"{P_BIOINF_TESTING}/TSO500/%s/",
                 "StG": False,
-                "subdir": r"Results/",
-        },
+                "subdir": r"metrics/",
+            },
         },
         **dict.fromkeys(["ArcherDX", "ONC"], False),
     },
@@ -233,8 +233,9 @@
             "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),
     },
-}}
+}