Merge branch 'dev' of ssh://git-r3lab-server.uni.lu:8022/shaman.narayanasamy/IMP into dev

rules/Analysis/MGMT.rules

@@ -137,19 +137,19 @@ rule ANALYSIS_MG_VARIANT_CALLING:
             echo "Indexing bam: {input[1]}"
             samtools index {input[1]}
         fi
-       
+
         if [[ ! -f {input[0]}.fai ]]
         then
           echo "Fasta index doesn't exist, Creating one..."
           echo "Indexing fasta: {input[0]}"
           samtools faidx {input[0]}
         fi
-        
+
         #temporary directory and files
         VCF_MPU=$(mktemp --tmpdir={TMPDIR} -t "XXXXXX.mpu.vcf")
         VCF_FRB=$(mktemp --tmpdir={TMPDIR} -t "XXXXXX.frb.vcf")
         VCF_PLT=$(mktemp --tmpdir={TMPDIR} -t "XXXXXX.plt.vcf")
-        
+
         ### run_mpileup {input[0]} {input[1]} {output[1]}
         echo "Running samtools mpileup"
         samtools mpileup -uf {input[0]} {input[1]} |\
@@ -208,19 +208,19 @@ rule ANALYSIS_MT_VARIANT_CALLING:
             echo "Indexing bam: {input[1]}"
             samtools index {input[1]}
         fi
-       
+
         if [[ ! -f {input[0]}.fai ]]
         then
           echo "Fasta index doesn't exist, Creating one..."
           echo "Indexing fasta: {input[0]}"
           samtools faidx {input[0]}
         fi
-        
+
         #temporary directory and files
         VCF_MPU=$(mktemp --tmpdir={TMPDIR} -t "XXXXXX.mpu.vcf")
         VCF_FRB=$(mktemp --tmpdir={TMPDIR} -t "XXXXXX.frb.vcf")
         VCF_PLT=$(mktemp --tmpdir={TMPDIR} -t "XXXXXX.plt.vcf")
-        
+
         ### run_mpileup {input[0]} {input[1]} {output[1]}
         echo "Running samtools mpileup"
         samtools mpileup -uf {input[0]} {input[1]} |\

rules/Util.rules

@@ -220,6 +220,18 @@ rule CHECK_TOOL_VERSION:
 #         python {SRCDIR}/make.pwy.hierarchy.kegg.py -o {output[1]}
 #        """
 
+rule _DOWNLOAD_TRIMMOMATIC_ADAPTERS:
+    output:
+        "{DBPATH}/adapters/adapters.done"
+    shell:
+        """
+        wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
+        unzip Trimmomatic-Src-0.32.zip
+        cp -r trimmomatic-0.32/adapters {DBPATH}
+        rm Trimmomatic-Src-0.32.zip && rm -rf trimmomatic-0.32
+        touch {output}
+        """
+
 rule _DOWNLOAD_KEGG_INFORMATION:
     log:
         U_LOG