From e1401cec74e3ed3121fa31a129ec1dae0f4cb8e4 Mon Sep 17 00:00:00 2001
From: jboom1 <j.boom.me@lumc.nl>
Date: Thu, 7 Nov 2019 09:24:58 +0100
Subject: [PATCH] Addressed PR comments.
---
CHANGELOG.md | 2 +-
minimap2.wdl | 9 ++++-----
2 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index dec1078..e323acd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,7 +11,7 @@ that users understand how the changes affect the new version.
version 2.1.0-dev
---------------------------
-+ Updated parameter_meta sections for Minimap2 and TranscriptClean.
++ Updated parameter_meta sections for Minimap2 and TranscriptClean to wdl-aid format.
+ Updated cores variable for TALON.
+ Updated TALON to version 4.4.
+ Added parameter_meta sections to the following tools:
diff --git a/minimap2.wdl b/minimap2.wdl
index df439a8..da570ec 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -96,18 +96,17 @@ task Mapping {
Int kmerSize = 15
Boolean outputSAM = false
String outputPrefix
+ Boolean addMDtagToSAM = false
+ Boolean secondaryAlignment = false
File referenceFile
File queryFile
Int? maxIntronLength
Int? maxFragmentLength
- Boolean? skipSelfAndDualMappings
Int? retainMaxSecondaryAlignments
Int? matchingScore
Int? mismatchPenalty
String? howToFindGTAG
- Boolean? addMDtagToSAM
- Boolean? secondaryAlignment
Int cores = 4
String memory = "30G"
@@ -122,6 +121,8 @@ task Mapping {
~{"-k " + kmerSize} \
~{true="-a" false="" outputSAM} \
~{"-o " + outputPrefix} \
+ ~{true="--MD" false="" addMDtagToSAM} \
+ --secondary=~{true="yes" false="no" secondaryAlignment} \
~{"-t " + cores} \
~{"-G " + maxIntronLength} \
~{"-F " + maxFragmentLength} \
@@ -130,8 +131,6 @@ task Mapping {
~{"-A " + matchingScore} \
~{"-B " + mismatchPenalty} \
~{"-u " + howToFindGTAG} \
- ~{true="--MD" false="" addMDtagToSAM} \
- --secondary=~{true="yes" false="no" secondaryAlignment} \
~{referenceFile} \
~{queryFile}
}
--
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