From 3f2e05cefca2a4f94d4a5fbcae420d6dda74e2ad Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Tue, 21 Apr 2015 10:57:10 +0200
Subject: [PATCH] rm datadir parameter
---
Snakefile | 1 -
rules/Preprocessing/MG.rules | 2 +-
rules/Preprocessing/MT.rules | 2 +-
3 files changed, 2 insertions(+), 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index 1e631fc..fed3c3c 100644
--- a/Snakefile
+++ b/Snakefile
@@ -41,7 +41,6 @@ if os.path.exists(CUSTOM_CONFIG_PATH):
SRCDIR = os.environ.get("SRCDIR", config['imp_src'])
# get parameters from the command line
-DATADIR = os.environ.get("DATADIR", config['datadir'])
OUTPUTDIR = os.environ.get("OUTPUTDIR", config['outputdir'])
MG = os.environ.get("MG", config['raws']['Metagenomics']).split()
MT = os.environ.get("MT", config['raws']['Metatranscriptomics']).split()
diff --git a/rules/Preprocessing/MG.rules b/rules/Preprocessing/MG.rules
index 9a4af10..a94b35d 100644
--- a/rules/Preprocessing/MG.rules
+++ b/rules/Preprocessing/MG.rules
@@ -2,7 +2,7 @@ rule PREPROCESSING_MG_GET_FILES:
message:
"Preparing MG DATA files : %s." % ', '.join(MG)
input:
- expand('{dir}/{raw}', raw=MG, dir=DATADIR)
+ MG
output:
expand('{dir}/{raw}', raw=['MG.R1.fq', 'MG.R2.fq'], dir=P_OUT)
benchmark:
diff --git a/rules/Preprocessing/MT.rules b/rules/Preprocessing/MT.rules
index 00a5241..429ea86 100644
--- a/rules/Preprocessing/MT.rules
+++ b/rules/Preprocessing/MT.rules
@@ -2,7 +2,7 @@ rule PREPROCESSING_MT_GET_FILES:
message:
"Preparing MT DATA files : %s." % ', '.join(MT)
input:
- expand('{dir}/{raw}', raw=MT, dir=DATADIR)
+ MT
output:
expand('{dir}/{raw}', raw=['MT.R1.fq', 'MT.R2.fq'], dir=P_OUT)
run:
--
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