From 865b9cf635d5f67b348a1b3181a9c5550626864c Mon Sep 17 00:00:00 2001
From: jaamarks <32715488+jaamarks@users.noreply.github.com>
Date: Mon, 20 May 2024 11:28:38 -0400
Subject: [PATCH] Fix error when setting case_control_gwas=true

Issue: When setting case_control_gwas = true in the config file, an error
       occurred due to a missing subject_level/gwas.txt file.

Cause: The gwas rule requires subject_level/gwas.txt as input. However,
       the script used by the agg_population_qc_tables rule generates
       this file, but it wasn't listed as an output.

Solution: This commit explicitly adds gwas.txt as an output of the
          agg_population_qc_tables rule, ensuring the gwas rule correctly
          waits for its dependency before execution.
---
 src/cgr_gwas_qc/workflow/sub_workflows/subject_qc.smk | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/cgr_gwas_qc/workflow/sub_workflows/subject_qc.smk b/src/cgr_gwas_qc/workflow/sub_workflows/subject_qc.smk
index 397ce871..1c338f4b 100644
--- a/src/cgr_gwas_qc/workflow/sub_workflows/subject_qc.smk
+++ b/src/cgr_gwas_qc/workflow/sub_workflows/subject_qc.smk
@@ -48,6 +48,7 @@ targets = [
     "subject_level/subjects.fam",
     "subject_level/concordance.csv",
     "subject_level/population_qc.csv",
+    "subject_level/gwas.txt",
     "subject_level/.population_plots.done",
     "subject_level/.control_plots.done",
     "delivery/gwas.assoc",
@@ -536,6 +537,7 @@ rule agg_population_qc_tables:
         population_qc_tables=_population_qc_tables,
     output:
         "subject_level/population_qc.csv",
+        "subject_level/gwas.txt",
     script:
         "../scripts/agg_population_qc_tables.py"