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Verified Commit 93c9b2e9 authored by Laurent Modolo's avatar Laurent Modolo
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gatk4: fix SelectVariants cmd (remove -T)

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src/nf_modules/gatk4/main.nf
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...@@ -56,7 +56,7 @@ process filter_indels { ...@@ -56,7 +56,7 @@ 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" SelectVariants \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
-selectType INDEL \ -selectType INDEL \
...@@ -79,7 +79,7 @@ process high_confidence_snp { ...@@ -79,7 +79,7 @@ process high_confidence_snp {
script: script:
xmx_memory = "${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" VariantFiltration \
-R ${fasta} \ -R ${fasta} \
-V ${vcf} \ -V ${vcf} \
--filterExpression "${high_confidence_snp_filter}" \ --filterExpression "${high_confidence_snp_filter}" \
......
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