From 021ace34a1123e27fe09b3ad07d88c861c58b6a1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 8 Mar 2021 17:34:41 +0100
Subject: [PATCH] gatk4: remove unnecessary -T option

---
 src/nf_modules/gatk4/main.nf | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 0a468ca5..f37f2808 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -15,7 +15,7 @@ process variant_calling {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \
+gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
   -nct ${task.cpus} \
   -R ${fasta} \
   -I ${bam} \
@@ -36,7 +36,7 @@ process filter_snp {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \
+gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
   -nct ${task.cpus} \
   -R ${fasta} \
   -V ${vcf} \
@@ -107,7 +107,7 @@ process high_confidence_indels {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T VariantFiltration \
+gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
   -nct ${task.cpus} \
   -R ${fasta} \
   -V ${vcf} \
@@ -130,7 +130,7 @@ process recalibrate_snp_table {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T BaseRecalibrator \
+gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
   -nct ${task.cpus} \
   -R ${fasta} \
   -I ${bam} \
@@ -154,7 +154,7 @@ process recalibrate_snp {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T PrintReads \
+gatk --java-options "-Xmx${xmx_memory}G" PrintReads \
   --use_jdk_deflater \
   --use_jdk_inflater \
   -nct ${task.cpus} \
@@ -178,7 +178,7 @@ process haplotype_caller {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \
+gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
   -nct ${task.cpus} \
   -R ${fasta} \
   -I ${bam} \
@@ -201,7 +201,7 @@ process gvcf_genotyping {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T GenotypeGVCFs \
+gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
   -nct ${task.cpus} \
   -R ${fasta} \
   -V ${gvcf} \
@@ -222,7 +222,7 @@ process select_variants_snp {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}GG" -T SelectVariants \
+gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
   -nct ${task.cpus} \
   -R ${fasta} \
   -V ${vcf} \
@@ -244,7 +244,7 @@ process select_variants_indels {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \
+gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
   -nct ${task.cpus} \
   -R ${fasta} \
   -V ${vcf} \
@@ -267,7 +267,7 @@ process personalized_genome {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
-gatk --java-options "-Xmx${xmx_memory}G" -T FastaAlternateReferenceMaker\
+gatk --java-options "-Xmx${xmx_memory}G" FastaAlternateReferenceMaker\
   -R ${reference} \
   -V ${vcf} \
   -o ${file_id[0]}_genome.fasta
-- 
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