updated versions for cnvkit and manta

Rules/cnvkit_germ.rl

@@ -3,4 +3,4 @@ rule cnvkit_germ:
     output: heatmap="cnvkit_out/cnvkit_heatmap.pdf"
     threads: 12
     params: cnvkitgenome=config['references'][pfamily]['CNVKITREF'],rname="pl:cnvkit"
-    shell: "mkdir -p cnvkit_out; cd cnvkit_out; module load cnvkit/0.8.5; cnvkit.py batch --scatter --method wgs -r {params.cnvkitgenome} -p {threads} ../*.recal.bam; cnvkit.py heatmap -d -o cnvkit_heatmap.pdf *.cns"
+    shell: "mkdir -p cnvkit_out; cd cnvkit_out; module load cnvkit/0.9.1; cnvkit.py batch --scatter --method wgs -r {params.cnvkitgenome} -p {threads} ../*.recal.bam; cnvkit.py heatmap -d -o cnvkit_heatmap.pdf *.cns"

Rules/cnvkit_somatic.rl

@@ -11,4 +11,4 @@ rule cnvkit_somatic:
             dir=config['project']['workpath']+"/cnvkit_out/{x}_cnvkit"
     params: vcfdir=config['project']['workpath']+"/germline_vcfs",tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],access=config['references'][pfamily]['CNVKITACCESS'],targets="cnvkit_targets.bed",antitargets="cnvkit_antitargets.bed",genome=config['references'][pfamily]['CNVKITGENOME'],regions="exome_targets.bed",snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:cnvkit_somatic"
     threads: 2
-    shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts  --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf} -L {params.regions}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.8.5; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.antitargets} -q 20 -o {output.dir}/{params.normalsample}.antitargetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {output.dir}/{params.normalsample}.antitargetcoverage.cnn -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr"
+    shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts  --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf} -L {params.regions}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.9.1; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.antitargets} -q 20 -o {output.dir}/{params.normalsample}.antitargetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {output.dir}/{params.normalsample}.antitargetcoverage.cnn -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr"

Rules/cnvkit_somatic_tumoronly.rl

@@ -7,4 +7,4 @@ rule cnvkit_somatic_tumoronly:
             dir=config['project']['workpath']+"/cnvkit_out/{x}_cnvkit"
     params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],access=config['references'][pfamily]['CNVKITACCESS'],targets="cnvkit_targets.bed",antitargets="cnvkit_antitargets.bed",genome=config['references'][pfamily]['CNVKITGENOME'],regions="exome_targets.bed",rname="pl:cnvkit_somatic"
     threads: 1
-    shell: "module load cnvkit/0.8.5; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py reference -f {params.genome} -o {output.dir}/{params.tumorsample}.FLATreference.cnn -t {params.targets} -a {params.antitargets}; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.tumorsample}.FLATreference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -i {params.tumorsample} -z -v {input.vcf} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -z -v {input.vcf} -i {params.tumorsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -i {params.tumorsample} -z -v {input.vcf} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr"
+    shell: "module load cnvkit/0.9.1; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py reference -f {params.genome} -o {output.dir}/{params.tumorsample}.FLATreference.cnn -t {params.targets} -a {params.antitargets}; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.tumorsample}.FLATreference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -i {params.tumorsample} -z -v {input.vcf} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -z -v {input.vcf} -i {params.tumorsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -i {params.tumorsample} -z -v {input.vcf} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr"

Rules/cnvkit_summary.rl

@@ -2,4 +2,4 @@ rule cnvkit_summary:
     input: cnvkit=expand(config['project']['workpath']+"/cnvkit_out/{p}_calls.cns",p=pairs)
     output: heatmap=config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf"
     params: rname="pl:cnvkit_summary"
-    shell: "module load cnvkit/0.8.5; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl"
+    shell: "module load cnvkit/0.9.1; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl"

Rules/cnvkit_summary_tumoronly.rl

@@ -2,4 +2,4 @@ rule cnvkit_summary_tumoronly:
     input: cnvkit=expand(config['project']['workpath']+"/cnvkit_out/{s}_calls.cns",s=samples)
     output: heatmap=config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",summary="cnvkit_out/AllCNValteredGenes.txt"
     params: rname="pl:cnvkit_summary"
-    shell: "module load cnvkit/0.8.5; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl"
+    shell: "module load cnvkit/0.9.1; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl"

Rules/cnvkit_wgs_somatic.rl

@@ -11,4 +11,4 @@ rule cnvkit_wgs_somatic:
 #            theta=config['project']['workpath']+"/cnvkit_out/{x}_thetaIN",
     params: vcfdir=config['project']['workpath']+"/germline_vcfs",tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],access=config['references'][pfamily]['CNVKITACCESS'],antitargets=config['references'][pfamily]['CNVKITANTITARGETS'],genome=config['references'][pfamily]['CNVKITGENOME'],snpsites=config['references'][pfamily]['SNPSITES'],targets=config['references'][pfamily]['CNVKITWGSTARGETS'],rname="pl:cnvkit"
     threads: 2
-    shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts  --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.8.5; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {params.antitargets} -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn --no-edge; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {params.antitargets} {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr --no-edge; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -p {threads} -t 1e-6 -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr"
+    shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts  --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.9.1; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {params.antitargets} -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn --no-edge; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {params.antitargets} {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr --no-edge; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -p {threads} -t 1e-6 -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr"

Rules/manta_germline.rl

@@ -7,9 +7,9 @@ rule manta_germline:
      run:
       fl=os.popen("ls *.recal.bam").read().split()      
       var=" --bam "+" --bam ".join(fl)
-      cmd="mkdir -p manta_out; module load manta; module load python/2.7; configManta.py --referenceFasta {params.genome} --exome --runDir {output.dir}"+var
+      cmd="mkdir -p manta_out; module load manta/1.2.0; module load python/2.7; configManta.py --referenceFasta {params.genome} --exome --runDir {output.dir}"+var
       print(cmd)
       shell(cmd)
-      cmd="module load python/2.7; {output.dir}/runWorkflow.py -m local -j {threads} -g 12"
+      cmd="module load manta/1.2.0; module load python/2.7; {output.dir}/runWorkflow.py -m local -j {threads} -g 12"
       print(cmd)
       shell(cmd)

Rules/manta_somatic.rl

@@ -4,4 +4,4 @@ rule manta_somatic:
      output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz",
      params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0], gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta_somatic"
      threads: 8
-     shell: "mkdir -p manta_out/{params.normalsample}+{params.tumorsample}; module load manta/1.1.0; module load python/2.7; configManta.py --bam={input.normal} --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.normalsample}+{params.tumorsample}; manta_out/{params.normalsample}+{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12"
+     shell: "mkdir -p manta_out/{params.normalsample}+{params.tumorsample}; module load manta/1.2.0; module load python/2.7; configManta.py --bam={input.normal} --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.normalsample}+{params.tumorsample}; manta_out/{params.normalsample}+{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12"

Rules/manta_somatic_tumoronly.rl

@@ -3,4 +3,4 @@ rule manta_somatic_tumoronly:
      output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz",
      params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta"
      threads: 8
-     shell: "mkdir -p manta_out/{params.tumorsample}; module load manta/1.1.0; module load python/2.7; configManta.py --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.tumorsample}; manta_out/{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12"
+     shell: "mkdir -p manta_out/{params.tumorsample}; module load manta/1.2.0; module load python/2.7; configManta.py --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.tumorsample}; manta_out/{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12"

Rules/manta_wgs.rl

@@ -7,9 +7,9 @@ rule manta_wgs:
      run:
       fl=os.popen("ls *.recal.bam").read().split()      
       var=" --bam "+" --bam ".join(fl)
-      cmd="mkdir -p manta_out; module load python/2.7; module load manta; configManta.py --referenceFasta {params.genome} --runDir {output.dir}"+var
+      cmd="mkdir -p manta_out; module load python/2.7; module load manta/1.2.0; configManta.py --referenceFasta {params.genome} --runDir {output.dir}"+var
       print(cmd)
       shell(cmd)
-      cmd="module load python/2.7; {output.dir}/runWorkflow.py -m local -j {threads} -g 12"
+      cmd="module load manta/1.2.0; module load python/2.7; {output.dir}/runWorkflow.py -m local -j {threads} -g 12"
       print(cmd)
       shell(cmd)