adding input options for trim and tbed option for strelka2

preproc_fastq/trimgalore.sh

@@ -25,12 +25,20 @@ shift $(($OPTIND -1))
 baseDir="`dirname \"$0\"`"
 
 # Check for mandatory options
-if [[ -z $pair_id ]] || [[ -z $fq1 ]]; then
+if [[ -z $pair_id ]]; then
     usage
 fi
-fqs=("$@")
+fqs=''
+i=0
 numfq=$#
 
+while [[ $i -le $numfq ]]
+do
+    fqs="$fqs $1"
+    i=$((i + 1))
+    shift 1
+done
+
 if [[ -f $fq1 ]]
 then
     fqs="$fq1"
@@ -50,11 +58,11 @@ module load trimgalore/0.6.4 cutadapt/2.5
 if [ $numfq > 1 ]
 then
     trim_galore --paired -q 25 --illumina --gzip --length 35 ${fqs}
-    mv ${r1base}_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
-    mv ${r2base}_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
+    mv *_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
+    mv *_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
 else
     trim_galore -q 25 --illumina --gzip --length 35 ${fqs}
-    mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
+    mv *_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
     cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz 
 fi
 

variants/germline_vc.sh

@@ -18,6 +18,7 @@ do
         p) pair_id=$OPTARG;;
         a) algo=$OPTARG;;
 	t) rna=1;;
+	b) tbed=$OPTARG;;
 	q) pon==$OPTARG;; 
         h) usage;;
     esac
@@ -131,6 +132,11 @@ then
 
 elif [[ $algo == 'strelka2' ]]
 then
+    opt=''
+    if [[ -n $tbed ]]
+    then
+	opt="--callRegions ${tbed}.gz"
+    fi
     if [[ $rna == 1 ]]
     then
 	mode="--rna"
@@ -143,7 +149,7 @@ then
     for i in *.bam; do
 	gvcflist="$gvcflist --bam ${i}"
     done
-    configManta.py $gvcflist --referenceFasta ${reffa} $mode --runDir manta
+    configManta.py $gvcflist $opt --referenceFasta ${reffa} $mode --runDir manta
     manta/runWorkflow.py -m local -j $NPROC
     if [[ -f manta/results/variants/candidateSmallIndels.vcf.gz ]]
     then

variants/somatic_vc.sh

@@ -93,11 +93,11 @@ module load htslib/gcc/1.8
 
 if [ $algo == 'strelka2' ]
 then
+    module load strelka/2.9.10 manta/1.3.1 samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14
     opt=''
     if [[ -n $tbed ]]
     then
-	opt="--callRegions ${tbed}.gz}"
-	module load strelka/2.9.10 manta/1.3.1 samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14
+	opt="--callRegions ${tbed}.gz"
     fi
     mkdir manta     
     configManta.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} $opt --runDir manta