From ac7a88b410cb6701e016f409a9f184b46da44553 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 11 Aug 2020 21:39:51 -0500
Subject: [PATCH] adding if is docker
---
alignment/bamqc.sh | 8 ++++++--
alignment/dnaseqalign.sh | 9 ++++++---
alignment/markdups.sh | 29 ++++++++++++++++++-----------
alignment/starfusion.sh | 7 +++++--
alignment/virusalign.sh | 7 +++++--
genect_rnaseq/geneabundance.sh | 7 +++++--
preproc_fastq/trimgalore.sh | 9 ++++++---
variants/checkmate.sh | 26 +++++++++++---------------
variants/cnvkit.sh | 9 +++++----
variants/gatkrunner.sh | 7 +++++--
variants/msisensor.sh | 1 -
variants/uni_norm_annot.sh | 9 +++++----
variants/union.sh | 10 ++++++----
13 files changed, 83 insertions(+), 55 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index acd91a8..cf2e3d6 100755
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -64,8 +64,12 @@ then
parseopt="$parseopt -r $index_path"
fi
tmpdir=`pwd`
-source /etc/profile.d/modules.sh
-module load samtools/gcc/1.10 fastqc/0.11.8 bedtools/2.29.0 picard/2.10.3
+
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load samtools/gcc/1.10 fastqc/0.11.8 bedtools/2.29.0 picard/2.10.3
+fi
samtools flagstat ${sbam} > ${pair_id}.flagstat.txt
fastqc -f bam ${sbam}
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index 14b2dc1..084b844 100755
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -51,13 +51,16 @@ else
testexe='/usr/local/bin'
fi
-source /etc/profile.d/modules.sh
-module load python/2.7.x-anaconda bwakit/0.7.15 samtools/gcc/1.8 picard/2.10.3
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load python/2.7.x-anaconda bwakit/0.7.15 samtools/gcc/1.8 picard/2.10.3 bwa/intel/0.7.17
+fi
baseDir="`dirname \"$0\"`"
diff $fq1 $fq2 > difffile
-module load bwa/intel/0.7.17
+
if [ -s difffile ]
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index dbe1b8e..15fec48 100755
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -48,17 +48,18 @@ fi
baseDir="`dirname \"$0\"`"
-source /etc/profile.d/modules.sh
-module load picard/2.10.3
-
-if [ $algo == 'sambamba' ]
+if [[ -z $isdocker ]]
then
- module load speedseq/20160506
- sambamba markdup -t $NPROC ${sbam} ${pair_id}.dedup.bam
- touch ${pair_id}.dedup.stat.txt
-elif [ $algo == 'samtools' ]
+ source /etc/profile.d/modules.sh
+ module load picard/2.10.3
+fi
+
+if [ $algo == 'samtools' ]
then
- module load samtools/gcc/1.8
+ if [[ -z $isdocker ]]
+ then
+ module load samtools/gcc/1.8
+ fi
samtools markdup -s --output-fmt BAM -@ $NPROC sort.bam ${pair_id}.dedup.bam
touch ${pair_id}.dedup.stat.txt
elif [ $algo == 'picard' ]
@@ -69,7 +70,10 @@ then
java -XX:ParallelGCThreads=$NPROC -Djava.io.tmpdir=./ -Xmx16g -jar $PICARD/picard.jar MarkDuplicates BARCODE_TAG=RX I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
elif [ $algo == 'fgbio_umi' ]
then
- module load fgbio bwakit/0.7.15 bwa/intel/0.7.17 samtools/gcc/1.8
+ if [[ -z $isdocker ]]
+ then
+ module load fgbio bwakit/0.7.15 bwa/intel/0.7.17 samtools/gcc/1.8
+ fi
samtools index -@ $NPROC ${sbam}
fgbio --tmp-dir ./ GroupReadsByUmi -s identity -i ${sbam} -o group.bam --family-size-histogram ${pair_id}.umihist.txt -e 0 -m 0
fgbio --tmp-dir ./ CallMolecularConsensusReads -i group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
@@ -90,5 +94,8 @@ then
else
cp ${sbam} ${pair_id}.dedup.bam
fi
-module load samtools/gcc/1.8
+if [[ -z $isdocker ]]
+then
+ module load samtools/gcc/1.8
+fi
samtools index -@ $NPROC ${pair_id}.dedup.bam
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 583dce5..9bc7050 100755
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -38,9 +38,12 @@ then
fi
baseDir="`dirname \"$0\"`"
-source /etc/profile.d/modules.sh
-module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
+fi
if [[ -n $method ]] && [[ $method == 'trinity' ]]
then
diff --git a/alignment/virusalign.sh b/alignment/virusalign.sh
index 6343ef9..7840d20 100755
--- a/alignment/virusalign.sh
+++ b/alignment/virusalign.sh
@@ -34,8 +34,11 @@ then
fi
reffa=${ref}/idt_virus_reference.fa
-source /etc/profile.d/modules.sh
-module load bwa/intel/0.7.17 picard/2.10.3 samtools/1.6
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load bwa/intel/0.7.17 picard/2.10.3 samtools/1.6
+fi
baseDir="`dirname \"$0\"`"
samtools view -@ 8 -b -u -F 2 ${bam} |samtools sort -n - >unmapped.bam
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index e70954a..bbaf11f 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -40,8 +40,11 @@ if [[ $NPROC > 64 ]]
then
NPROC=64
fi
-source /etc/profile.d/modules.sh
-module load subread/1.6.1
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load subread/1.6.1
+fi
baseDir="`dirname \"$0\"`"
export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index e198d3c..aadd30e 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -55,9 +55,12 @@ if [[ $numfq == 1 ]]
then
copts="$copts --paired"
fi
-
-source /etc/profile.d/modules.sh
-module load trimgalore/0.6.4 cutadapt/2.5
+
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load trimgalore/0.6.4 cutadapt/2.5
+fi
trim_galore $copts ${fqs}
files=`find ./ -name "*_val_1.fq.gz"`
diff --git a/variants/checkmate.sh b/variants/checkmate.sh
index 6bdb0cf..855b168 100755
--- a/variants/checkmate.sh
+++ b/variants/checkmate.sh
@@ -28,17 +28,23 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
shift $(($OPTIND -1))
baseDir="`dirname \"$0\"`"
-# Check for mandatory options
-source /etc/profile.d/modules.sh
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:/usr/local/bin/:$PATH
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load samtools/gcc/1.8 bcftools/gcc/1.8
+ ncm=/project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py
+fi
-module load samtools/gcc/1.8 bcftools/gcc/1.8
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:/usr/local/bin/:$PATH
+if [[ -f /usr/local/bin/ncm.py ]]
+then
+ ncm=/usr/local/bin/ncm.py
+fi
if [[ -z $capture ]]
then
capture="${index_path}/NGSCheckMate.bed"
fi
-
if [[ -f "${index_path}/genome.fa" ]]
then
reffa="${index_path}/genome.fa"
@@ -50,15 +56,5 @@ for i in *.bam; do
bcftools mpileup -A -d 1000000 -C50 -Ou --gvcf 0 -f ${reffa} -T ${capture} $i | bcftools call -m --gvcf 0 -Ov | bcftools convert --gvcf2vcf -f ${reffa} -Ov -o ${prefix}.vcf
done
-if [[ -f /project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py ]]
-then
- ncm=/project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py
-elif [[ -f /usr/local/bin/ncm.py ]]
-then
- ncm=/usr/local/bin/ncm.py
-else
- echo "ncm missing"
-fi
-
python $ncm -V -d ./ -bed $capture -O ./ -N ${pair_id}
perl $baseDir/sequenceqc_somatic.pl -i ${pair_id}_all.txt -o ${pair_id}.sequence.stats.txt
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index bb9ea27..dc37f05 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -63,8 +63,11 @@ capture="$paneldir/targetpanel.bed"
targets="$paneldir/cnvkit."
normals="$paneldir/pon.cnn"
-source /etc/profile.d/modules.sh
-module load cnvkit/0.9.5 bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 java/oracle/jdk1.8.0_171 snpeff/4.3q
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load cnvkit/0.9.5 bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 java/oracle/jdk1.8.0_171 snpeff/4.3q
+fi
if [[ -f "${paneldir}/pon.downsample.cnn" ]]
then
@@ -100,8 +103,6 @@ fi
if [[ $numsnps -gt 100 ]]
then
- #samtools index ${sbam}
- #java -jar /cm/shared/apps/gatk/3.8/target/package/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ${reffa} --output_mode EMIT_ALL_SITES -L ${index_path}/IDT_snps.hg38.bed -o common_variants.vcf -glm BOTH -dcov 10000 -I ${sbam}
bcftools mpileup -A -d 1000000 -C50 -Ou --gvcf 0 -f ${reffa} -a INFO/AD,INFO/ADF,INFO/ADR,FORMAT/DP,FORMAT/SP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR -T ${index_path}/IDT_snps.hg38.bed ${sbam} | bcftools call -m --gvcf 0 -Ov | bcftools convert --gvcf2vcf -f ${reffa} -Ov -o common_variants.vcf
$baseDir/formatVcfCNV.pl cnvkit_common common_variants.vcf
echo -e "CHROM\tPOS\tAO\tRO\tDP\tMAF" > ${pair_id}.ballelefreq.txt
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index 01533a2..26509fd 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -49,8 +49,11 @@ then
usage
fi
-source /etc/profile.d/modules.sh
-module load gatk/4.1.4.0 samtools/gcc/1.8
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load gatk/4.1.4.0 samtools/gcc/1.8
+fi
which samtools
samtools index -@ $NPROC ${sbam}
diff --git a/variants/msisensor.sh b/variants/msisensor.sh
index 1ab0aba..1d27dc8 100755
--- a/variants/msisensor.sh
+++ b/variants/msisensor.sh
@@ -30,7 +30,6 @@ if [[ -z $sbam ]] || [[ -z $index_path ]]; then
usage
fi
-source /etc/profile.d/modules.sh
export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
bedopt=''
diff --git a/variants/uni_norm_annot.sh b/variants/uni_norm_annot.sh
index e47e045..502fa0e 100755
--- a/variants/uni_norm_annot.sh
+++ b/variants/uni_norm_annot.sh
@@ -37,10 +37,11 @@ if [[ -z $snpeffgeno ]]
then
snpeffgeno='GRCh38.86'
fi
-
-source /etc/profile.d/modules.sh
-module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
-
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
+fi
export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
diff --git a/variants/union.sh b/variants/union.sh
index a02cd2c..1b58f5f 100755
--- a/variants/union.sh
+++ b/variants/union.sh
@@ -26,11 +26,13 @@ echo $pair_id $index_path $dir
if [[ -z $dir ]]
then
-dir='.'
+ dir='.'
+fi
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
fi
-
-source /etc/profile.d/modules.sh
-module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
HS=${dir}/*.hotspot.vcf.gz
list1=`ls ${dir}/*vcf.gz|grep -v hotspot`
--
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