From a8a06cd70cfd14eff770da4c04878635932794c8 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gail.com>
Date: Tue, 13 Mar 2018 15:36:15 +0100
Subject: [PATCH] add star task
---
.gitignore | 1 +
star.wdl | 37 +++++++++++++++++++++++++++++++++++++
2 files changed, 38 insertions(+)
create mode 100644 .gitignore
create mode 100644 star.wdl
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..9f11b75
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.idea/
diff --git a/star.wdl b/star.wdl
new file mode 100644
index 0000000..7c8c4c9
--- /dev/null
+++ b/star.wdl
@@ -0,0 +1,37 @@
+task Star {
+ String? preCommand
+
+ File inputR1
+ File? inputR2
+ String genomeDir
+ String outFileNamePrefix
+
+ String? outSAMtype = "BAM SortedByCoordinate"
+ String? readFilesCommand = "zcat"
+ Int? runThreadN
+ String? outStd
+ String? twopassMode
+ String? outSAMattrRGline
+
+ Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"} #needs to be extended for all possible values
+
+ command {
+ set -e -o pipefail
+ mkdir -p ${sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")}
+ ${preCommand}
+ STAR \
+ --readFilesIn ${inputR1} ${inputR2} \
+ --outFileNamePrefix ${outFileNamePrefix} \
+ --genomeDir ${genomeDir} \
+ ${"--readFilesCommand " + readFilesCommand} \
+ ${"--outSAMtype " + outSAMtype} \
+ ${"--runThreadN " + runThreadN} \
+ ${"--outStd " + outStd} \
+ ${"--twopassMode " + twopassMode} \
+ ${"--outSAMattrRGline " + outSAMattrRGline}
+ }
+
+ output {
+ File bamFile = outFileNamePrefix + "Aligned." + samOutputNames["${outSAMtype}"]
+ }
+}
\ No newline at end of file
--
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