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GATK/Getpileupsummaries: If no intervals use variants instead (#1787)

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If no intervals use variants instead
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FriederikeHanssen 2022-06-16 15:00:01 +02:00 committed by GitHub
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modules/gatk4/getpileupsummaries/main.nf
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@ -25,7 +25,7 @@ process GATK4_GETPILEUPSUMMARIES {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def interval_command = intervals ? "--intervals $intervals" : "" def interval_command = intervals ? "--intervals $intervals" : "--intervals $variants"
def reference_command = fasta ? "--reference $fasta" : '' def reference_command = fasta ? "--reference $fasta" : ''
def avail_mem = 3 def avail_mem = 3