From 12f57bca1ca926935d177d0ba41badd6f7453c55 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 2 Jun 2020 10:35:19 -0500
Subject: [PATCH] adding input options for trim and tbed option for strelka2
---
preproc_fastq/trimgalore.sh | 18 +++++++++++++-----
variants/germline_vc.sh | 8 +++++++-
variants/somatic_vc.sh | 4 ++--
3 files changed, 22 insertions(+), 8 deletions(-)
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index 8bd5613..36e64d5 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/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 ${pair_id}.trim.R2.fastq.gz
fi
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 9f598d9..38ce8ee 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -18,6 +18,7 @@ do
p) pair_id=$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
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index a8b0594..b6ec609 100755
--- a/variants/somatic_vc.sh
+++ b/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
--
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