From cb854d983ba960975ffbfe59508682ba042faa36 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 20 Aug 2018 14:26:28 +0200
Subject: [PATCH] add seqstat generate
---
biopet/seqstat.wdl | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
create mode 100644 biopet/seqstat.wdl
diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl
new file mode 100644
index 0000000..2009975
--- /dev/null
+++ b/biopet/seqstat.wdl
@@ -0,0 +1,40 @@
+task Generate {
+ input {
+ String? preCommand
+ File? toolJar
+ File fastqR1
+ File fastqR2
+ String outputFile
+ String? sample
+ String? library
+ String? readgroup
+
+ Int memory = 4
+ Float memoryMultiplier = 2.0
+ }
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-seqstat -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ mkdir -p $(dirname ~{outputFile})
+ ~{toolCommand} \
+ --fastqR1 ~{fastqR1} \
+ --fastqR2 ~{fastqR2} \
+ --output ~{outputFile} \
+ ~{"--sample " + sample} \
+ ~{"--library " + library } \
+ ~{"--readgroup " + readgroup }
+ }
+
+ output {
+ File json = outputFile
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
\ No newline at end of file
--
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