From 34ac04e262d51c63649e9472fa258e62807ce23d Mon Sep 17 00:00:00 2001
From: kehillio <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 13 May 2019 16:43:16 +0200
Subject: [PATCH] add possibility to change ref path to rules in config files
---
workflows/simple_metaphlan2/SnakeFile | 8 ++++----
workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile | 6 +++---
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/SnakeFile
index 8f93995..37c6ca8 100644
--- a/workflows/simple_metaphlan2/SnakeFile
+++ b/workflows/simple_metaphlan2/SnakeFile
@@ -1,10 +1,10 @@
configfile: "config.yaml"
# ==== Rule paths ====
-__metaphlan2_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
-__metaphlan2_merge_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
-__metaphlan2_heatmap_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
-__graphlan_from_metaphlan2_rules = "../subworkflows/graphlan_from_metaphlan2/SnakeFile"
+__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/metaphlan2.rules")
+__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules")
+__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules")
+__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
__input_dir = config['input_dir']
__main_output_dir = config.get('output_dir', 'output')
diff --git a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
index dfd7278..d7ba774 100644
--- a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
+++ b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
@@ -8,9 +8,9 @@ This subworkflow need to be called to be used by specifying:
"""
# ==== Rule paths ====
-__export2graphlan_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
-__graphlan_annotate_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
-__graphlan_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
+__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/metaphlan2.rules")
+__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules")
+__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules")
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
--
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