From 8f5612b1df49152d3b592667ccb0b54e64e83c47 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Thu, 12 Jun 2025 14:46:03 +0200
Subject: [PATCH] wip sinffles

---
 sniffles2.wdl | 55 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 sniffles2.wdl

diff --git a/sniffles2.wdl b/sniffles2.wdl
new file mode 100644
index 00000000..6849a47e
--- /dev/null
+++ b/sniffles2.wdl
@@ -0,0 +1,55 @@
+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
+	}
+}