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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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James A. Fellows Yates 2022-06-09 08:33:37 +02:00 committed by GitHub
parent 939653a47e
commit 70f7f07a37
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1 changed files with 2 additions and 2 deletions
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modules/gatk/indelrealigner/main.nf
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@ -26,7 +26,7 @@ process GATK_INDELREALIGNER {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def known = known_vcf ? "-known ${known_vcf}" : "" def known = known_vcf ? "-known ${known_vcf}" : ""
if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
def avail_mem = 3 def avail_mem = 3
if (!task.memory) { if (!task.memory) {
@ -40,7 +40,7 @@ process GATK_INDELREALIGNER {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
-T IndelRealigner \\ -T IndelRealigner \\
-R ${fasta} \\ -R ${fasta} \\
-I ${input} \\ -I ${bam} \\
--targetIntervals ${intervals} \\ --targetIntervals ${intervals} \\
${known} \\ ${known} \\
-o ${prefix}.bam \\ -o ${prefix}.bam \\