diff --git a/gatk.wdl b/gatk.wdl index 88904be59e660f32d57ec543f394054c727b6f1a..c00af93a591e3787249363669a1dfbd38f355e17 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -1575,15 +1575,15 @@ task VariantEval { String javaXmx = "4G" # TODO: Refine estimate. For now 4 minutes per GB of input. Int timeMinutes = ceil(size(flatten([evalVcfs, comparisonVcfs]), "G") * 4) - String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0" + String dockerImage = "quay.io/biocontainers/gatk4:4.1.7.0--py38_0" } command { set -e mkdir -p "$(dirname ~{outputPath})" gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \ - VariantFiltration \ - -O ~{outputPath} \ + VariantEval \ + --output ~{outputPath} \ ~{true="--eval" false="" length(evalVcfs) > 0} ~{sep=" --eval " evalVcfs} \ ~{true="--comparison" false="" length(comparisonVcfs) > 0} ~{sep=" --comparison " comparisonVcfs} \ ~{"-R " + referenceFasta} \