From cd18ce6a03823e8b09229bddf0f1dcd9ac7a1fdb Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Fri, 3 Jul 2020 10:26:38 +0200
Subject: [PATCH] Address comments.
---
CHANGELOG.md | 3 ++-
talon.wdl | 2 +-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 69a57b1..9a54671 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,7 +11,8 @@ that users understand how the changes affect the new version.
version 4.0.0-develop
---------------------------
-+ TALON: Update `FilterTalonTranscripts` to new version.
++ TALON: Update `FilterTalonTranscripts` to new version, which removes the
+ pairingsFile and replaces this with datasetsFile.
+ TALON: Add `GetSpliceJunctions` & `LabelReads` tasks.
+ TALON: Update to version 5.0.
+ Add tasks for pbmm2, the PacBio wrapper for minimap2.
diff --git a/talon.wdl b/talon.wdl
index c70850d..87fc407 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -280,7 +280,7 @@ task GetSpliceJunctions {
SJinformationFile: {description: "TALON GTF file or database from which to extract exons/introns.", category: "required"}
inputFileType: {description: "The file type of SJinformationFile.", category: "required"}
referenceGTF: {description: "GTF reference file (ie GENCODE).", category: "required"}
- runMode: {description: "Determines whether to include introns or exons in the output.", category: "required"}
+ runMode: {description: "Determines whether to include introns or exons in the output.", category: "common"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
--
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