From 1c28f624326c54e2dfc084d01fd3a44b1ae24491 Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Mon, 17 Aug 2015 10:45:40 +0200
Subject: [PATCH] some debug
---
IMP | 2 +-
init.rule | 2 +-
rules/Preprocessing/MG.rules | 4 +---
rules/Preprocessing/MT.rules | 3 +--
4 files changed, 4 insertions(+), 7 deletions(-)
diff --git a/IMP b/IMP
index 0547a6e..172543f 100755
--- a/IMP
+++ b/IMP
@@ -17,7 +17,7 @@ __doc__ = """Integrated Metaomic Pipeline.
Usage:
IMP [-m MG1 -m MG2] [-t MT1 -t MT2] -o OUTPUT [--enter] [--norm] [--ask] [-n CONTAINER] [-c CONFIGFILE] [-d DBPATH] [-e ENV] ... [COMMANDS ...]
- IMP --init [-d DBPATH]
+ IMP --init [-d DBPATH] [-n CONTAINER]
IMP (-h | --help)
IMP --version
diff --git a/init.rule b/init.rule
index 55944d3..950a09a 100644
--- a/init.rule
+++ b/init.rule
@@ -107,7 +107,7 @@ rule INDEX_FASTA_FILE:
"{fasta}.ann"
shell:
"""
- bwa index {wildcards.fasta} > {log} 2>&1
+ bwa index {wildcards.fasta}
"""
diff --git a/rules/Preprocessing/MG.rules b/rules/Preprocessing/MG.rules
index 0b230b1..27930bf 100644
--- a/rules/Preprocessing/MG.rules
+++ b/rules/Preprocessing/MG.rules
@@ -40,9 +40,7 @@ rule PREPROCESSING_MG_TRIM:
shell:
"""
java -jar {config[trimmomatic][jarfile]} PE -threads {THREADS} {input[0]} {input[1]} {output} \
- ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}-PE.fa:\
- {config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:\
- {config[trimmomatic][simple_clip_threshold]} \
+ ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}-PE.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
LEADING:{config[trimmomatic][leading]} \
TRAILING:{config[trimmomatic][trailing]} \
SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \
diff --git a/rules/Preprocessing/MT.rules b/rules/Preprocessing/MT.rules
index 990a159..e2fd94b 100644
--- a/rules/Preprocessing/MT.rules
+++ b/rules/Preprocessing/MT.rules
@@ -23,8 +23,7 @@ rule PREPROCESSING_MT_TRIM:
shell:
"""
java -jar {config[trimmomatic][jarfile]} PE -threads {THREADS} {input[0]} {input[1]} {output} \
- ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}-PE.fa:{config[trimmomatic][seed_mismatch]}:\
- {config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
+ ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}-PE.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
LEADING:{config[trimmomatic][leading]} TRAILING:{config[trimmomatic][trailing]} \
SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \
MINLEN:{config[trimmomatic][minlen]} \
--
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