nf-core_modules/modules/gatk4/cnnscorevariants/main.nf

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process GATK4_CNNSCOREVARIANTS {
tag "$meta.id"
label 'process_low'
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//Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
if (params.enable_conda) {
exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."
}
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container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
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input:
tuple val(meta), path(vcf), path(aligned_input), path(intervals)
path fasta
path fai
path dict
path architecture
path weights
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def aligned_input = aligned_input ? "--input $aligned_input" : ""
def interval_command = intervals ? "--intervals $intervals" : ""
def architecture = architecture ? "--architecture $architecture" : ""
def weights = weights ? "--weights $weights" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK CnnScoreVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
--variant $vcf \\
--output ${prefix}.vcf.gz \\
--reference $fasta \\
$interval_command \\
$aligned_input \\
$architecture \\
$weights \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}