From 8712a6ed5b521712832e7b562302d66543f6cf7e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 12 Aug 2020 11:23:07 -0500
Subject: [PATCH] fb parallel options for BioHPC/Cloud
---
alignment/rnaseqalign.sh | 53 ++++++++++++++++++++++++++++++----------
variants/germline_vc.sh | 7 +++---
2 files changed, 44 insertions(+), 16 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index a46a1f7..1e590c9 100755
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -29,12 +29,16 @@ done
shift $(($OPTIND -1))
# Check for mandatory options
-if [[ -z $pair_id ]] || [[ -z $fq1 ]]; then
+if [[ -z $pair_id ]]
+then
usage
fi
-source /etc/profile.d/modules.sh
-module load samtools/1.6 picard/2.10.3
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load samtools/1.6 picard/2.10.3
+fi
baseDir="`dirname \"$0\"`"
NPROC=$SLURM_CPUS_ON_NODE
if [[ -z $NPROC ]]
@@ -42,28 +46,51 @@ then
NPROC=`nproc`
fi
+fqs=''
+i=0
+numfq=${#fqs[@]}
+while [[ $i -le $numfq ]]
+do
+ fqs="$fqs $1"
+ i=$((i + 1))
+ shift 1
+done
+hisat_opt=''
diff $fq1 $fq2 > difffile
+if [[ -f $fq1 ]]
+then
+ fqs="$fq1"
+fi
+if [[ -f $fq2 ]] && [[ -s difffile ]]
+then
+ fqs+=" $fq2"
+fi
+numfq=${#fqs[@]}
+
+star_opt=$fqs
+fqarray=($fqs)
+if [[ $numfq == 1 ]]
+then
+ hisat_opt="-1 ${fqarray[0]} -2 ${fqarray[1]}"
+else
+ hisat_opt="-U $fqarray[0]"
+fi
if [ $algo == 'star' ]
then
- if [ -s difffile ]
+ if [[ -z $isdocker ]]
then
module load star/2.4.2a
- STAR --genomeDir ${index_path}/star_index/ --readFilesIn $fq1 $fq2 --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out
- else
- module load star/2.4.2a
- STAR --genomeDir ${index_path}/star_index/ --readFilesIn $fq1 --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out
fi
+ STAR --genomeDir ${index_path}/star_index/ --readFilesIn $star_opt --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out
mv outLog.final.out ${pair_id}.alignerout.txt
mv outAligned.sortedByCoord.out.bam ${pair_id}.bam
else
- module load hisat2/2.1.0-intel
- if [ -s difffile ]
+ if [[ -z $isdocker ]]
then
- hisat2 -p $NPROC --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
- else
- hisat2 -p $NPROC --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
+ module load hisat2/2.1.0-intel
fi
+ hisat2 -p $NPROC --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/genome $hisat_opt -S out.sam --summary-file ${pair_id}.alignerout.txt
if [[ $umi == 1 ]]
then
python ${baseDir}/add_umi_sam.py -s out.sam -o output.bam
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index ab1e772..59c5d05 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -86,14 +86,15 @@ then
if [[ -z $isdocker ]]
then
module load freebayes/gcc/1.2.0 parallel/20150122
+ paropt="--delay 2 -j $NPROC"
+ else
+ paropt="--delay 1 --jobs 0 --memfree 2G"
fi
bamlist=''
for i in *.bam; do
bamlist="$bamlist --bam ${PWD}/${i}"
done
- #--memfree 2G for DNANexus
-
- cut -f 1 $fbsplit | parallel --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
+ cut -f 1 $fbsplit | parallel ${paropt} "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.fb.vcf.gz -
elif [[ $algo == 'platypus' ]]
then
--
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