From 52c704d8c3d8547dfff0b1759586fa1809ec3528 Mon Sep 17 00:00:00 2001
From: kehillio <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 13 May 2019 17:37:47 +0200
Subject: [PATCH] fix Snakefile names
---
.../graphlan/export2graphlan/{SnakeFile => Snakefile} | 0
tools/graphlan/graphlan/{SnakeFile => Snakefile} | 0
.../graphlan_annotate/{SnakeFile => Snakefile} | 0
tools/metaphlan2/metaphlan2/{SnakeFile => Snakefile} | 0
tools/metaphlan2/metaphlan2/usage_example.rules | 2 +-
.../metaphlan2_heatmap/{SnakeFile => Snakefile} | 0
.../metaphlan2/metaphlan2_heatmap/usage_example.rules | 2 +-
.../metaphlan2_merge/{SnakeFile => Snakefile} | 0
tools/metaphlan2/metaphlan2_merge/usage_example.rules | 2 +-
workflows/simple_metaphlan2/{SnakeFile => Snakefile} | 10 +++++-----
workflows/{subworfklows => subworkflows}/README.md | 0
.../graphlan_from_metaphlan2/Snakefile} | 6 +++---
12 files changed, 11 insertions(+), 11 deletions(-)
rename tools/graphlan/export2graphlan/{SnakeFile => Snakefile} (100%)
rename tools/graphlan/graphlan/{SnakeFile => Snakefile} (100%)
rename tools/graphlan/graphlan_annotate/{SnakeFile => Snakefile} (100%)
rename tools/metaphlan2/metaphlan2/{SnakeFile => Snakefile} (100%)
rename tools/metaphlan2/metaphlan2_heatmap/{SnakeFile => Snakefile} (100%)
rename tools/metaphlan2/metaphlan2_merge/{SnakeFile => Snakefile} (100%)
rename workflows/simple_metaphlan2/{SnakeFile => Snakefile} (89%)
rename workflows/{subworfklows => subworkflows}/README.md (100%)
rename workflows/{subworfklows/graphlan_from_metaphlan2/SnakeFile => subworkflows/graphlan_from_metaphlan2/Snakefile} (86%)
diff --git a/tools/graphlan/export2graphlan/SnakeFile b/tools/graphlan/export2graphlan/Snakefile
similarity index 100%
rename from tools/graphlan/export2graphlan/SnakeFile
rename to tools/graphlan/export2graphlan/Snakefile
diff --git a/tools/graphlan/graphlan/SnakeFile b/tools/graphlan/graphlan/Snakefile
similarity index 100%
rename from tools/graphlan/graphlan/SnakeFile
rename to tools/graphlan/graphlan/Snakefile
diff --git a/tools/graphlan/graphlan_annotate/SnakeFile b/tools/graphlan/graphlan_annotate/Snakefile
similarity index 100%
rename from tools/graphlan/graphlan_annotate/SnakeFile
rename to tools/graphlan/graphlan_annotate/Snakefile
diff --git a/tools/metaphlan2/metaphlan2/SnakeFile b/tools/metaphlan2/metaphlan2/Snakefile
similarity index 100%
rename from tools/metaphlan2/metaphlan2/SnakeFile
rename to tools/metaphlan2/metaphlan2/Snakefile
diff --git a/tools/metaphlan2/metaphlan2/usage_example.rules b/tools/metaphlan2/metaphlan2/usage_example.rules
index 4b7e091..b4e995a 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: "SnakeFile"
+include: "Snakefile"
rule all:
input:
diff --git a/tools/metaphlan2/metaphlan2_heatmap/SnakeFile b/tools/metaphlan2/metaphlan2_heatmap/Snakefile
similarity index 100%
rename from tools/metaphlan2/metaphlan2_heatmap/SnakeFile
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 3d9acd0..0c74a9e 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: "SnakeFile"
+include: "Snakefile"
rule all:
input:
diff --git a/tools/metaphlan2/metaphlan2_merge/SnakeFile b/tools/metaphlan2/metaphlan2_merge/Snakefile
similarity index 100%
rename from tools/metaphlan2/metaphlan2_merge/SnakeFile
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 dd2f986..5dfda11 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: "SnakeFile"
+include: "Snakefile"
rule all:
input:
diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/Snakefile
similarity index 89%
rename from workflows/simple_metaphlan2/SnakeFile
rename to workflows/simple_metaphlan2/Snakefile
index 5a7b2c0..a53b037 100644
--- a/workflows/simple_metaphlan2/SnakeFile
+++ b/workflows/simple_metaphlan2/Snakefile
@@ -1,10 +1,10 @@
configfile: "config.yaml"
# ==== Rule paths ====
-__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")
+__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']
__main_output_dir = config.get('output_dir', 'output')
@@ -39,7 +39,7 @@ include: __metaphlan2_heatmap_rules
# ---- Graphlan Dendogram
__graphlan_from_metaphlan2_output_dir = __main_output_dir + "/graphlan"
-__graphlan_from_metaphlan2_output_file_name = config['graphlan_from_metaphlan2'].get('output_name',"dendogram.png")
+__graphlan_from_metaphlan2_output_file_name = config.get("graphlan_from_metaphlan2", {}).get('output_name',"dendogram.png")
__graphlan_from_metaphlan2_input = __metaphlan2_merge_output
__graphlan_from_metaphlan2_output = "{dir}/{file_name}".format(dir=__graphlan_from_metaphlan2_output_dir,
file_name=__graphlan_from_metaphlan2_output_file_name)
diff --git a/workflows/subworfklows/README.md b/workflows/subworkflows/README.md
similarity index 100%
rename from workflows/subworfklows/README.md
rename to workflows/subworkflows/README.md
diff --git a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile b/workflows/subworkflows/graphlan_from_metaphlan2/Snakefile
similarity index 86%
rename from workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
rename to workflows/subworkflows/graphlan_from_metaphlan2/Snakefile
index 0614069..ee86962 100644
--- a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
+++ b/workflows/subworkflows/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/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_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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