add path and list for sumstats

ht-diva · Jul 8, 2024 · cf5f4d5 · cf5f4d5
1 parent e41d06d
commit cf5f4d5
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -6,9 +6,10 @@ run:
 # paths
 workspace_path: 'results'
 destination_path: 'destination'
-sumstats_path: 'config/local.txt'
+
 
 # LB
+sumstats_list: 'config/local.txt'
 path_code: "workflow/scripts/"
 labels:
   chr_label: "'#CHR'"
@@ -32,6 +33,7 @@ thresholds:
   hole: 250000
 
 # MR
+sumstats_path: '/exchange/healthds/pQTL/results/META_CHRIS_INTERVAL/qced_sumstats_digits_not_flipped/output'
 mapping_filepath: 'data/MR/mapped_gene_file_GRCh37_21052025.txt'
 array_list_path: "data/MR/"
 params:

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -4,7 +4,7 @@ import pandas as pd
 
 # Define input for the rules
 data = []
-with open(config["sumstats_path"], "r") as fp:
+with open(config["sumstats_list"], "r") as fp:
     lines = fp.readlines()
 
 for line in lines: