From fefa29bef864475c8d5b3e3f0cf7f605fc854c09 Mon Sep 17 00:00:00 2001
From: Richard Zetterberg <richard.zetterberg@gmail.com>
Date: Wed, 18 May 2022 09:34:03 +0200
Subject: [PATCH] Resolves #34

Makes sure `--config` is passed on to `gwas.py` commands
---
 gwas/gwas.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gwas/gwas.py b/gwas/gwas.py
index 06d000c6..39d3be8c 100644
--- a/gwas/gwas.py
+++ b/gwas/gwas.py
@@ -390,7 +390,7 @@ def make_regenie_merge_commands(args, logistic):
     cmd = ''
     for pheno in args.pheno:
         cmd += '$PYTHON gwas.py merge-regenie ' + \
-            pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno']) + \
+            pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno', 'config']) + \
             ' --sumstats {out}_chr@_{pheno}.regenie'.format(out=args.out, pheno=pheno) + \
             ' --basename {out}_chr@'.format(out=args.out) + \
             ' --out {out}_{pheno} '.format(out=args.out, pheno=pheno) + \
@@ -403,7 +403,7 @@ def make_saige_merge_commands(args, logistic, array_spec):
     use_chunks = (args.chunk_size_bp is not None)
     for pheno in args.pheno:
         cmd += '$PYTHON gwas.py merge-saige ' + \
-            pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno']) + \
+            pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno', 'config']) + \
             (' --sumstats {out}_chr@_{pheno}.saige'.format(out=args.out, pheno=pheno) if (not use_chunks) else "") + \
             (' --sumstats {out}_chunk@_{pheno}.saige'.format(out=args.out, pheno=pheno) if use_chunks else "") + \
             ' --basename {out}_chr@'.format(out=args.out) + \
@@ -417,7 +417,7 @@ def make_plink2_merge_commands(args, logistic):
     cmd = ''
     for pheno in args.pheno:
         cmd += '$PYTHON gwas.py merge-plink2 ' + \
-            pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno']) + \
+            pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno', 'config']) + \
             ' --sumstats {out}_chr@.{pheno}.glm.{what}'.format(out=args.out, pheno=pheno, what=('logistic' if logistic else 'linear')) + \
             ' --basename {out}_chr@'.format(out=args.out) + \
             ' --out {out}_{pheno} '.format(out=args.out, pheno=pheno) + \