some debug

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
 

init.rule

@@ -107,7 +107,7 @@ rule INDEX_FASTA_FILE:
         "{fasta}.ann"
     shell:
         """
-        bwa index {wildcards.fasta} > {log} 2>&1
+        bwa index {wildcards.fasta}
         """
 
 

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]} \

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]} \