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[WIP] sinffles2 #344

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[WIP] sinffles2 #344

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55 changes: 55 additions & 0 deletions sniffles2.wdl
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version 1.0

task Sniffles {
input {
File bam
File bamIndex
File? referenceFasta
File? tandemRepeats
File? genotypeVcfs

String outputVcf = "output.vcf"
String options = " "

Boolean mosaic = false
Boolean outputRnames = false

Int threads = 4
String memory = "32GiB" # 16 was fine without --no-qc
Int timeMinutes = 1 + ceil(size(bam, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/sniffles:2.6.2--pyhdfd78af_0"
}

meta {
citation: {
doi: "10.1038/s41587-023-02024-y"
}
}

command {
set -e
mkdir -p "$(dirname ~{outputVcf})"

sniffles \
~{"--reference " + referenceFasta} \
~{"--tandem-repeats " + tandemRepeats} \
~{"--genotype-vcf " + genotypeVcfs} \
--threads ~{threads} \
~{true="--output-rnames" false="" outputRnames} \
~{true="--mosaic" false="" mosaic} \
--input ~{bam} \
~{options} \
--vcf ~{outputVcf}
}

output {
File vcf = outputVcf
}

runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
}
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