Commit b4a6ad0e authored by Sander Bollen's avatar Sander Bollen
Browse files

remove extraneous backslashes

parent 73040388
......@@ -180,7 +180,7 @@ rule sickle:
r2 = temp(out_path("{sample}/pre_process/{sample}.trimmed_R2.fastq")),
s = out_path("{sample}/pre_process/{sample}.trimmed_singles.fastq"),
conda: "envs/sickle.yml"
shell: "sickle pe -f {input.r1} -r {input.r2} -t sanger -o {output.r1} " \
shell: "sickle pe -f {input.r1} -r {input.r2} -t sanger -o {output.r1} "
"-p {output.r2} -s {output.s}"
rule cutadapt:
......@@ -192,7 +192,7 @@ rule cutadapt:
r1 = temp(out_path("{sample}/pre_process/{sample}.cutadapt_R1.fastq")),
r2 = temp(out_path("{sample}/pre_process/{sample}.cutadapt_R2.fastq"))
conda: "envs/cutadapt.yml"
shell: "cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -m 1 -o {output.r1} " \
shell: "cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -m 1 -o {output.r1} "
"{input.r1} -p {output.r2} {input.r2}"
rule align:
......@@ -205,8 +205,8 @@ rule align:
rg = "@RG\\tID:{sample}_lib1\\tSM:{sample}\\tPL:ILLUMINA"
output: temp(out_path("{sample}/bams/{sample}.sorted.bam"))
conda: "envs/bwa.yml"
shell: "bwa mem -t 8 -R '{params.rg}' {input.ref} {input.r1} {input.r2} " \
"| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null " \
shell: "bwa mem -t 8 -R '{params.rg}' {input.ref} {input.r1} {input.r2} "
"| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null "
"INPUT=/dev/stdin OUTPUT={output} SORT_ORDER=coordinate"
rule markdup:
......@@ -218,9 +218,9 @@ rule markdup:
bam = out_path("{sample}/bams/{sample}.markdup.bam"),
metrics = out_path("{sample}/bams/{sample}.markdup.metrics")
conda: "envs/picard.yml"
shell: "picard MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} " \
"INPUT={input.bam} OUTPUT={output.bam} " \
"METRICS_FILE={output.metrics} " \
shell: "picard MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
"INPUT={input.bam} OUTPUT={output.bam} "
"METRICS_FILE={output.metrics} "
"MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=500"
rule baserecal:
......@@ -236,11 +236,11 @@ rule baserecal:
output:
grp = out_path("{sample}/bams/{sample}.baserecal.grp")
conda: "envs/gatk.yml"
shell: "{input.java} -jar {input.gatk} -T BaseRecalibrator " \
"-I {input.bam} -o {output.grp} -nct 8 -R {input.ref} " \
"-cov ReadGroupCovariate -cov QualityScoreCovariate " \
"-cov CycleCovariate -cov ContextCovariate -knownSites " \
"{input.dbsnp} -knownSites {input.one1kg} " \
shell: "{input.java} -jar {input.gatk} -T BaseRecalibrator "
"-I {input.bam} -o {output.grp} -nct 8 -R {input.ref} "
"-cov ReadGroupCovariate -cov QualityScoreCovariate "
"-cov CycleCovariate -cov ContextCovariate -knownSites "
"{input.dbsnp} -knownSites {input.one1kg} "
"-knownSites {input.hapmap}"
rule gvcf_scatter:
......@@ -256,10 +256,10 @@ rule gvcf_scatter:
output:
gvcf=out_path("{sample}/vcf/{sample}.{chunk}.part.vcf.gz")
conda: "envs/gatk.yml"
shell: "java -jar -Xmx4G {input.gatk} -T HaplotypeCaller -ERC GVCF -I "\
"{input.bam} -R {input.ref} -D {input.dbsnp} "\
"-L '{params.chunk}' -o '{output.gvcf}' "\
"-variant_index_type LINEAR -variant_index_parameter 128000 " \
shell: "java -jar -Xmx4G {input.gatk} -T HaplotypeCaller -ERC GVCF -I "
"{input.bam} -R {input.ref} -D {input.dbsnp} "
"-L '{params.chunk}' -o '{output.gvcf}' "
"-variant_index_type LINEAR -variant_index_parameter 128000 "
"-BQSR {input.bqsr}"
......@@ -276,8 +276,8 @@ rule gvcf_gather:
output:
gvcf=out_path("{sample}/vcf/{sample}.g.vcf.gz")
conda: "envs/gatk.yml"
shell: "java -Xmx4G -cp {input.gatk} org.broadinstitute.gatk.tools.CatVariants "\
"-R {input.ref} -V '{params.gvcfs}' -out {output.gvcf} "\
shell: "java -Xmx4G -cp {input.gatk} org.broadinstitute.gatk.tools.CatVariants "
"-R {input.ref} -V '{params.gvcfs}' -out {output.gvcf} "
"-assumeSorted"
......@@ -295,7 +295,7 @@ rule genotype_scatter:
output:
vcf=out_path("multisample/genotype.{chunk}.part.vcf.gz")
conda: "envs/gatk.yml"
shell: "java -jar -Xmx4G {input.gatk} -T GenotypeGVCFs -R {input.ref} "\
shell: "java -jar -Xmx4G {input.gatk} -T GenotypeGVCFs -R {input.ref} "
"-V {params.li} -L '{params.chunk}' -o '{output.vcf}'"
......@@ -312,8 +312,8 @@ rule genotype_gather:
output:
combined=out_path("multisample/genotyped.vcf.gz")
conda: "envs/gatk.yml"
shell: "java -Xmx4G -cp {input.gatk} org.broadinstitute.gatk.tools.CatVariants "\
"-R {input.ref} -V '{params.vcfs}' -out {output.combined} "\
shell: "java -Xmx4G -cp {input.gatk} org.broadinstitute.gatk.tools.CatVariants "
"-R {input.ref} -V '{params.vcfs}' -out {output.combined} "
"-assumeSorted"
......@@ -443,8 +443,8 @@ rule covstats:
covj=out_path("{sample}/coverage/{bed}.covstats.json"),
covp=out_path("{sample}/coverage/{bed}.covstats.png")
conda: "envs/covstat.yml"
shell: "bedtools coverage -sorted -g {input.genome} -a {input.bed} -b {input.bam} " \
"-d | python {input.covpy} - --plot {output.covp} " \
shell: "bedtools coverage -sorted -g {input.genome} -a {input.bed} -b {input.bam} "
"-d | python {input.covpy} - --plot {output.covp} "
"--title 'Targets coverage' --subtitle '{params.subt}' > {output.covj}"
......@@ -479,10 +479,10 @@ rule collectstats:
output:
out_path("{sample}/{sample}.stats.json")
conda: "envs/collectstats.yml"
shell: "python {input.colpy} --sample-name {params.sample_name} " \
"--pre-qc-fastq {input.preqc} --post-qc-fastq {input.postq} " \
"--mapped-num {input.mnum} --mapped-basenum {input.mbnum} " \
"--unique-num {input.unum} --usable-basenum {input.ubnum} " \
shell: "python {input.colpy} --sample-name {params.sample_name} "
"--pre-qc-fastq {input.preqc} --post-qc-fastq {input.postq} "
"--mapped-num {input.mnum} --mapped-basenum {input.mbnum} "
"--unique-num {input.unum} --usable-basenum {input.ubnum} "
"--female-threshold {params.fthresh} {input.cov} > {output}"
rule merge_stats:
......
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