removed hard coded paths to seqprg; update GATK to 4.1.4

alignment/dnaseqalign.sh

@@ -44,7 +44,12 @@ then
     read_group=$pair_id
 fi
 
-testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
+if [[ $index_path == *project* ]]
+then
+    testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
+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

alignment/markdups.sh

@@ -39,8 +39,14 @@ then
     index_path="/project/shared/bicf_workflow_ref/human/grch38_cloud/dnaref"
 fi
 
+if [[ $index_path == *project* ]]
+then
+    testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
+else
+    testexe='/usr/local/bin'
+fi
+
 baseDir="`dirname \"$0\"`"
-testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
 
 source /etc/profile.d/modules.sh
 module load picard/2.10.3

genect_rnaseq/geneabundance.sh

@@ -40,6 +40,7 @@ then
 fi
 source /etc/profile.d/modules.sh
 module load subread/1.6.1
+
 export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 featureCounts -s $stranded -M --fraction -J --ignoreDup -T $NPROC -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}

variants/gatkrunner.sh

@@ -58,7 +58,7 @@ else
 fi
 
 source /etc/profile.d/modules.sh
-module load gatk/4.1.2.0 samtools/gcc/1.8
+module load gatk/4.1.4.0 samtools/gcc/1.8
 which samtools
 /cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $NPROC ${sbam}
 

variants/itdseek.sh

@@ -52,12 +52,12 @@ else
 fi
 
 source /etc/profile.d/modules.sh	
-
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 module load samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14 htslib/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 
 stexe=`which samtools`
 
-samtools view -@ $NPROC -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
+samtools view -@ $NPROC -L ${itdbed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
 tabix ${pair_id}.itdseek.vcf.gz
 bcftools norm --fasta-ref $reffa -c w -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config $snpeffgeno - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
 

variants/svcalling.sh

@@ -58,6 +58,7 @@ fi
 
 source /etc/profile.d/modules.sh	
 module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 if [[ $method == 'delly' ]]
 then
@@ -100,9 +101,9 @@ if [[ $method == 'svaba' ]]
 then
     if [[ -n ${normal} ]]
     then
-	/project/shared/bicf_workflow_ref/seqprg/svaba/bin/svaba run -p $NPROC -G ${reffa} -t ${sbam} -n ${normal} -a ${pair_id}
+	svaba run -p $NPROC -G ${reffa} -t ${sbam} -n ${normal} -a ${pair_id}
     else
-	/project/shared/bicf_workflow_ref/seqprg/svaba/bin/svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
+	svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
     fi
     vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf | vcf-sort -t temp > svaba.unfiltered.vcf
     bash $baseDir/norm_annot.sh -r ${index_path} -p svaba -v svaba.unfiltered.vcf -s

variants/uni_norm_annot.sh

@@ -41,6 +41,8 @@ fi
 source /etc/profile.d/modules.sh
 module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q 
 
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
+
 perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
 mv ${vcf} ${pair_id}.ori.vcf.gz
 bgzip -f ${pair_id}.uniform.vcf
@@ -48,5 +50,5 @@ j=${pair_id}.uniform.vcf.gz
 tabix -f $j
 bcftools norm --fasta-ref $reffa -m - -Oz $j -o ${pair_id}.norm.vcf.gz
 bash $baseDir/annotvcf.sh -p ${pair_id} -r $index_path -v ${pair_id}.norm.vcf.gz -g $snpeffgeno
-/project/shared/bicf_workflow_ref/seqprg/vt/vt decompose_blocksub ${pair_id}.annot.vcf.gz -p -a -o ${pair_id}.vcf
+vt decompose_blocksub ${pair_id}.annot.vcf.gz -p -a -o ${pair_id}.vcf
 bgzip -f ${pair_id}.vcf