From a8314de9c3a2746eb44bf041fe1849c49241e547 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 19 Feb 2021 16:30:52 +0100
Subject: [PATCH] add -c to stringtie
---
stringtie.wdl | 3 +++
1 file changed, 3 insertions(+)
diff --git a/stringtie.wdl b/stringtie.wdl
index d3a6f73..9c2f3cf 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -31,6 +31,7 @@ task Stringtie {
Boolean? firstStranded
Boolean? secondStranded
String? geneAbundanceFile
+ Float? minimumCoverage
Int threads = 1
String memory = "2G"
@@ -47,6 +48,7 @@ task Stringtie {
~{true="-e" false="" skipNovelTranscripts} \
~{true="--rf" false="" firstStranded} \
~{true="--fr" false="" secondStranded} \
+ ~{"-c " + minimumCoverage} \
-o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \
~{bam}
@@ -74,6 +76,7 @@ task Stringtie {
firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
+ minimumCoverage: {description: "The minimum coverage for a transcript to be shown in the output.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
--
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