adding updates formatting

alignment/markdups.sh

@@ -39,7 +39,7 @@ module load picard/2.10.3 samtools/1.6
 if [ $algo == 'sambamba' ]
 then
     module load speedseq/20160506
-    sambamba markdup -t $SLURM_CPUS_ON_NODE -r ${sbam} ${pair_id}.dedup.bam
+    sambamba markdup -t $SLURM_CPUS_ON_NODE ${sbam} ${pair_id}.dedup.bam
 elif [ $algo == 'samtools' ]
 then
     module load samtools/1.6

variants/germline_vc.sh

@@ -112,7 +112,7 @@ then
     else
 	mode="--exome"
     fi
-    module load strelka/2.8.3 samtools/1.6 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
+    module load strelka/2.9.0 samtools/1.6 manta/1.3.1 snpeff/4.3q vcftools/0.1.14
     mkdir manta strelka
     gvcflist=''
     for i in *.bam; do

variants/somatic_vc.sh

@@ -83,7 +83,7 @@ source /etc/profile.d/modules.sh
 
 if [ $algo == 'strelka2' ]
   then
-    module load strelka/2.8.3 samtools/1.6 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
+    module load strelka/2.9.0 samtools/1.6 manta/1.3.1 snpeff/4.3q vcftools/0.1.14
     mkdir manta strelka
     configManta.py --normalBam ${mnormal} --tumorBam ${mtumor} --referenceFasta ${reffa} --runDir manta
     manta/runWorkflow.py -m local -j 8