Address comments.

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.

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"}