From 9b5fbe320a4c5fbdabdce3c5b98398e278d44bc9 Mon Sep 17 00:00:00 2001
From: kehillio <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 13 May 2019 17:04:33 +0200
Subject: [PATCH] rename all as SnakeFile
---
.../export2graphlan/{export2graphlan.rules => SnakeFile} | 0
tools/graphlan/graphlan/{graphlan.rules => SnakeFile} | 0
.../{graphlan_annotate.rules => SnakeFile} | 0
tools/metaphlan2/metaphlan2/{metaphlan2.rules => SnakeFile} | 0
tools/metaphlan2/metaphlan2/usage_example.rules | 2 +-
.../{metaphlan2_heatmap.rules => SnakeFile} | 0
tools/metaphlan2/metaphlan2_heatmap/usage_example.rules | 2 +-
.../metaphlan2_merge/{metaphlan2_merge.rules => SnakeFile} | 0
tools/metaphlan2/metaphlan2_merge/usage_example.rules | 2 +-
workflows/simple_metaphlan2/SnakeFile | 6 +++---
workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile | 6 +++---
11 files changed, 9 insertions(+), 9 deletions(-)
rename tools/graphlan/export2graphlan/{export2graphlan.rules => SnakeFile} (100%)
rename tools/graphlan/graphlan/{graphlan.rules => SnakeFile} (100%)
rename tools/graphlan/graphlan_annotate/{graphlan_annotate.rules => SnakeFile} (100%)
rename tools/metaphlan2/metaphlan2/{metaphlan2.rules => SnakeFile} (100%)
rename tools/metaphlan2/metaphlan2_heatmap/{metaphlan2_heatmap.rules => SnakeFile} (100%)
rename tools/metaphlan2/metaphlan2_merge/{metaphlan2_merge.rules => SnakeFile} (100%)
diff --git a/tools/graphlan/export2graphlan/export2graphlan.rules b/tools/graphlan/export2graphlan/SnakeFile
similarity index 100%
rename from tools/graphlan/export2graphlan/export2graphlan.rules
rename to tools/graphlan/export2graphlan/SnakeFile
diff --git a/tools/graphlan/graphlan/graphlan.rules b/tools/graphlan/graphlan/SnakeFile
similarity index 100%
rename from tools/graphlan/graphlan/graphlan.rules
rename to tools/graphlan/graphlan/SnakeFile
diff --git a/tools/graphlan/graphlan_annotate/graphlan_annotate.rules b/tools/graphlan/graphlan_annotate/SnakeFile
similarity index 100%
rename from tools/graphlan/graphlan_annotate/graphlan_annotate.rules
rename to tools/graphlan/graphlan_annotate/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2/metaphlan2.rules b/tools/metaphlan2/metaphlan2/SnakeFile
similarity index 100%
rename from tools/metaphlan2/metaphlan2/metaphlan2.rules
rename to tools/metaphlan2/metaphlan2/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2/usage_example.rules b/tools/metaphlan2/metaphlan2/usage_example.rules
index c60f198..4b7e091 100644
--- a/tools/metaphlan2/metaphlan2/usage_example.rules
+++ b/tools/metaphlan2/metaphlan2/usage_example.rules
@@ -19,7 +19,7 @@ __metaphlan2_input = "{dir}/{sample}.{ext}".format(dir=__input_dir,
ext=__metaphlan2_input_type + ".gz")
__metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
sample="{sample}")
-include: "metaphlan2.rules"
+include: "SnakeFile"
rule all:
input:
diff --git a/tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules b/tools/metaphlan2/metaphlan2_heatmap/SnakeFile
similarity index 100%
rename from tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules
rename to tools/metaphlan2/metaphlan2_heatmap/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules b/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
index eb273ee..3d9acd0 100644
--- a/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
+++ b/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
@@ -17,7 +17,7 @@ __metaphlan2_heatmap_output_file_name = config['metaphlan2_heatmap'].get('output
__metaphlan2_heatmap_input = __input
__metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatmap_output_dir,
file_name=__metaphlan2_heatmap_output_file_name)
-include: "metaphlan2_heatmap.rules"
+include: "SnakeFile"
rule all:
input:
diff --git a/tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules b/tools/metaphlan2/metaphlan2_merge/SnakeFile
similarity index 100%
rename from tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules
rename to tools/metaphlan2/metaphlan2_merge/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2_merge/usage_example.rules b/tools/metaphlan2/metaphlan2_merge/usage_example.rules
index e1ba12a..dd2f986 100644
--- a/tools/metaphlan2/metaphlan2_merge/usage_example.rules
+++ b/tools/metaphlan2/metaphlan2_merge/usage_example.rules
@@ -21,7 +21,7 @@ __metaphlan2_merge_input = expand("{dir}/{sample}.txt".format(dir=__input_dir,
sample=config['samples'])
__metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
file_name=__metaphlan2_merge_output_file_name)
-include: "metaphlan2_merge.rules"
+include: "SnakeFile"
rule all:
input:
diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/SnakeFile
index 37c6ca8..5a7b2c0 100644
--- a/workflows/simple_metaphlan2/SnakeFile
+++ b/workflows/simple_metaphlan2/SnakeFile
@@ -1,9 +1,9 @@
configfile: "config.yaml"
# ==== Rule paths ====
-__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")
+__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/SnakeFile")
+__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/SnakeFile")
+__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/SnakeFile")
__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
__input_dir = config['input_dir']
diff --git a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
index d7ba774..0614069 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 = 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_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/SnakeFile")
+__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/SnakeFile")
+__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/SnakeFile")
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
--
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