From b92dbc90f497da5d30b68ee08b17e67cd20e79ee Mon Sep 17 00:00:00 2001
From: huzuner <hamdiyeuzuner@gmail.com>
Date: Thu, 17 Oct 2024 23:47:02 +0000
Subject: [PATCH 1/4] fix: fix excluding events from the report

---
 workflow/rules/common.smk | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 9aee5b52..c4ad6aa8 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -150,20 +150,7 @@ def get_final_output(wildcards):
                         expand(
                             "results/datavzrd-report/{batch}.{event}.{calling_type}.fdr-controlled",
                             batch=get_report_batches(calling_type),
-                            event=get_calling_events(calling_type),
-                            calling_type=calling_type,
-                        )
-                    )
-                else:
-                    final_output.extend(
-                        expand(
-                            "results/final-calls/{group}.{event}.{calling_type}.fdr-controlled.bcf",
-                            group=(
-                                variants_groups
-                                if calling_type == "variants"
-                                else fusions_groups
-                            ),
-                            event=get_calling_events(calling_type),
+                            event=event,
                             calling_type=calling_type,
                         )
                     )

From b530bb4df6683dafeca2a116dd08770000ca2de0 Mon Sep 17 00:00:00 2001
From: huzuner <hamdiyeuzuner@gmail.com>
Date: Fri, 18 Oct 2024 00:01:05 +0000
Subject: [PATCH 2/4] fix: restore else statement

---
 workflow/rules/common.smk | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index c4ad6aa8..6fd8d06e 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -154,6 +154,19 @@ def get_final_output(wildcards):
                             calling_type=calling_type,
                         )
                     )
+                else:
+                    final_output.extend(
+                        expand(
+                            "results/final-calls/{group}.{event}.{calling_type}.fdr-controlled.bcf",
+                            group=(
+                                variants_groups
+                                if calling_type == "variants"
+                                else fusions_groups
+                            ),
+                            event=event,
+                            calling_type=calling_type,
+                        )
+                    )
         else:
             final_output.extend(
                 expand(

From e6518e3370115009194a239b9b73708d9dd22ff2 Mon Sep 17 00:00:00 2001
From: Hamdiye Uzuner <hamdiyeuzuner@gmail.com>
Date: Fri, 18 Oct 2024 11:17:42 +0200
Subject: [PATCH 3/4] chore

---
 workflow/rules/common.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 6fd8d06e..3a29dd20 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -140,7 +140,7 @@ def get_final_output(wildcards):
 
     for calling_type in calling_types:
         if config["report"]["activate"]:
-            for event in config["calling"]["fdr-control"]["events"]:
+            for event in get_calling_events(calling_type):
                 if lookup(
                     dpath=f"calling/fdr-control/events/{event}/report",
                     within=config,

From 0b43367625d39e0fd6655ee0af3bf837dc996959 Mon Sep 17 00:00:00 2001
From: Hamdiye Uzuner <hamdiyeuzuner@gmail.com>
Date: Mon, 21 Oct 2024 10:42:50 +0200
Subject: [PATCH 4/4] fix: add report activation option to the simple test

---
 .test/config-simple/config.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.test/config-simple/config.yaml b/.test/config-simple/config.yaml
index 16e808ff..8548e31c 100644
--- a/.test/config-simple/config.yaml
+++ b/.test/config-simple/config.yaml
@@ -50,6 +50,7 @@ calling:
     local: true
     events: 
       present:
+        report: false
         varlociraptor: 
           - x
           - y