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Verified Commit 8e3c7bf4 authored by Laurent Modolo's avatar Laurent Modolo
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gatk4: fix java-options

parent 342d3265
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...@@ -15,7 +15,7 @@ process variant_calling { ...@@ -15,7 +15,7 @@ process variant_calling {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \
--spark-master local[${task.cpus}] \ --spark-master local[${task.cpus}] \
-R ${fasta} \ -R ${fasta} \
-I ${bam} \ -I ${bam} \
...@@ -36,7 +36,7 @@ process filter_snp { ...@@ -36,7 +36,7 @@ process filter_snp {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" SelectVariants \ gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
-selectType SNP \ -selectType SNP \
...@@ -57,7 +57,7 @@ process filter_indels { ...@@ -57,7 +57,7 @@ process filter_indels {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G"-T SelectVariants \ gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
-selectType INDEL \ -selectType INDEL \
...@@ -80,7 +80,7 @@ process high_confidence_snp { ...@@ -80,7 +80,7 @@ process high_confidence_snp {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G"-T VariantFiltration \ gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
--filterExpression "${high_confidence_snp_filter}" \ --filterExpression "${high_confidence_snp_filter}" \
...@@ -104,7 +104,7 @@ process high_confidence_indels { ...@@ -104,7 +104,7 @@ process high_confidence_indels {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" VariantFiltration \ gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
--filterExpression "${high_confidence_indel_filter}" \ --filterExpression "${high_confidence_indel_filter}" \
...@@ -126,7 +126,7 @@ process recalibrate_snp_table { ...@@ -126,7 +126,7 @@ process recalibrate_snp_table {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" BaseRecalibratorSpark \ gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibratorSpark \
--spark-master local[${task.cpus}] \ --spark-master local[${task.cpus}] \
-R ${fasta} \ -R ${fasta} \
-I ${bam} \ -I ${bam} \
...@@ -150,7 +150,7 @@ process recalibrate_snp { ...@@ -150,7 +150,7 @@ process recalibrate_snp {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" PrintReads \ gatk --java-options "-Xmx${xmx_memory}G" PrintReads \
--use_jdk_deflater \ --use_jdk_deflater \
--use_jdk_inflater \ --use_jdk_inflater \
-R ${fasta} \ -R ${fasta} \
...@@ -173,7 +173,7 @@ process haplotype_caller { ...@@ -173,7 +173,7 @@ process haplotype_caller {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \
--spark-master local[${task.cpus}] \ --spark-master local[${task.cpus}] \
-R ${fasta} \ -R ${fasta} \
-I ${bam} \ -I ${bam} \
...@@ -196,7 +196,7 @@ process gvcf_genotyping { ...@@ -196,7 +196,7 @@ process gvcf_genotyping {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" GenotypeGVCFs \ gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
-R ${fasta} \ -R ${fasta} \
-V ${gvcf} \ -V ${gvcf} \
-O ${file_id}_joint.vcf -O ${file_id}_joint.vcf
...@@ -216,7 +216,7 @@ process select_variants_snp { ...@@ -216,7 +216,7 @@ process select_variants_snp {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}GG" SelectVariants \ gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
--spark-master local[${task.cpus}] \ --spark-master local[${task.cpus}] \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
...@@ -238,7 +238,7 @@ process select_variants_indels { ...@@ -238,7 +238,7 @@ process select_variants_indels {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" SelectVariants \ gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
--spark-master local[${task.cpus}] \ --spark-master local[${task.cpus}] \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
...@@ -261,7 +261,7 @@ process personalized_genome { ...@@ -261,7 +261,7 @@ process personalized_genome {
script: script:
xmx_memory = "${task.memory}" - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-Options "-Xmx${xmx_memory}G" FastaAlternateReferenceMaker\ gatk --java-options "-Xmx${xmx_memory}G" FastaAlternateReferenceMaker\
-R ${reference} \ -R ${reference} \
-V ${vcf} \ -V ${vcf} \
-O ${file_id[0]}_genome.fasta -O ${file_id[0]}_genome.fasta
......
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