From 92c8725fc597743e7aa4b65ddec79f3e0bd872b3 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Fri, 12 Jun 2020 10:38:14 +0200
Subject: [PATCH] Add new STAR options.
---
CHANGELOG.md | 2 ++
star.wdl | 15 +++++++++++++--
2 files changed, 15 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2d4267c..61f4760 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 4.0.0-develop
---------------------------
++ STAR: Add options regarding alignment score and read length for tweaking when
+ processing rRNA depleted samples.
+ TALON: Update `minimumIdentity` to correct type (float, was integer)
& set new default according to developers (0.8, was 0).
+ Added bcftools stats task.
diff --git a/star.wdl b/star.wdl
index 8e6a511..6d80e9d 100644
--- a/star.wdl
+++ b/star.wdl
@@ -95,6 +95,10 @@ task Star {
String outFileNamePrefix
String outSAMtype = "BAM SortedByCoordinate"
String readFilesCommand = "zcat"
+ Int outFilterScoreMin = 0
+ Float outFilterScoreMinOverLread = 0.66
+ Int outFilterMatchNmin = 0
+ Float outFilterMatchNminOverLread = 0.66
String? outStd
String? twopassMode = "Basic"
Array[String]? outSAMattrRGline
@@ -119,6 +123,10 @@ task Star {
--genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \
--outSAMtype ~{outSAMtype} \
--readFilesCommand ~{readFilesCommand} \
+ --outFilterScoreMin ~{outFilterScoreMin} \
+ --outFilterScoreMinOverLread ~{outFilterScoreMinOverLread} \
+ --outFilterMatchNmin ~{outFilterMatchNmin} \
+ --outFilterMatchNminOverLread ~{outFilterMatchNminOverLread} \
~{"--outSAMunmapped " + outSAMunmapped} \
~{"--runThreadN " + runThreadN} \
~{"--outStd " + outStd} \
@@ -146,6 +154,10 @@ task Star {
outFileNamePrefix: {description: "The prefix for the output files. May include directories.", category: "required"}
outSAMtype: {description: "The type of alignment file to be produced. Currently only `BAM SortedByCoordinate` is supported.", category: "advanced"}
readFilesCommand: {description: "Equivalent to star's `--readFilesCommand` option.", category: "advanced"}
+ outFilterScoreMin: {description: "Equivalent to star's `--outFilterScoreMin` option.", category: "advanced"}
+ outFilterScoreMinOverLread: {description: "Equivalent to star's `--outFilterScoreMinOverLread` option.", category: "advanced"}
+ outFilterMatchNmin: {description: "Equivalent to star's `--outFilterMatchNmin` option.", category: "advanced"}
+ outFilterMatchNminOverLread: {description: "Equivalent to star's `--outFilterMatchNminOverLread` option.", category: "advanced"}
outStd: {description: "Equivalent to star's `--outStd` option.", category: "advanced"}
twopassMode: {description: "Equivalent to star's `--twopassMode` option.", category: "advanced"}
outSAMattrRGline: {description: "The readgroup lines for the fastq pairs given (in the same order as the fastq files).", category: "common"}
@@ -154,8 +166,7 @@ task Star {
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
--
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