Fix line length

UMCUGenetics · May 24, 2022 · 3a945bc · 3a945bc
1 parent d9c3db1
commit 3a945bc
Showing 1 changed file with 27 additions and 5 deletions.
diff --git a/GATK/4.2.1.0/VariantFiltration.nf b/GATK/4.2.1.0/VariantFiltration.nf
@@ -15,12 +15,34 @@ process VariantFiltrationSnpIndel {
         ext_vcf = params.compress || vcf_file.getExtension() == ".gz" ? ".vcf.gz" : ".vcf"
         ext_vcf_index = params.compress || vcf_file.getExtension() == ".gz" ? ".tbi" : ".idx"
         """
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants --reference ${params.genome} --variant $vcf_file --output ${vcf_file.simpleName}.snp${ext_vcf} --select-type-to-exclude INDEL
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants --reference ${params.genome} --variant $vcf_file --output ${vcf_file.simpleName}.indel${ext_vcf} --select-type-to-include INDEL
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants \
+        --reference ${params.genome} \
+        --variant $vcf_file \
+        --output ${vcf_file.simpleName}.snp${ext_vcf} \
+        --select-type-to-exclude INDEL
 
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration --reference ${params.genome} --variant ${vcf_file.simpleName}.snp${ext_vcf} --output ${vcf_file.simpleName}.snp_filter${ext_vcf} ${params.snp_filter} ${params.snp_cluster}
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration --reference ${params.genome} --variant ${vcf_file.simpleName}.indel${ext_vcf} --output ${vcf_file.simpleName}.indel_filter${ext_vcf} ${params.indel_filter}
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" SelectVariants \
+        --reference ${params.genome} \
+        --variant $vcf_file \
+        --output ${vcf_file.simpleName}.indel${ext_vcf} \
+        --select-type-to-include INDEL
 
-        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" MergeVcfs --INPUT ${vcf_file.simpleName}.snp_filter${ext_vcf} --INPUT ${vcf_file.simpleName}.indel_filter${ext_vcf} --OUTPUT ${vcf_file.simpleName}.filter${ext_vcf}
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration \
+        --reference ${params.genome} \
+        --variant ${vcf_file.simpleName}.snp${ext_vcf} \
+        --output ${vcf_file.simpleName}.snp_filter${ext_vcf} \
+        ${params.snp_filter} \
+        ${params.snp_cluster}
+
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" VariantFiltration \
+        --reference ${params.genome} \
+        --variant ${vcf_file.simpleName}.indel${ext_vcf} \
+        --output ${vcf_file.simpleName}.indel_filter${ext_vcf} \
+        ${params.indel_filter}
+
+        gatk --java-options "-Xmx${task.memory.toGiga()-4}G" MergeVcfs \
+        --INPUT ${vcf_file.simpleName}.snp_filter${ext_vcf} \
+        --INPUT ${vcf_file.simpleName}.indel_filter${ext_vcf} \
+        --OUTPUT ${vcf_file.simpleName}.filter${ext_vcf}
         """
 }