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gffcompare.wdl

@@ -144,13 +144,13 @@ task GffCompare {
         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"}
 
         # outputs
-        annotated: {description: ""}
+        annotated: {description: "Annotated GTF file."}
         loci: {description: ""}
-        stats: {description: ""}
-        tracking: {description: ""}
-        allFiles: {description: ""}
-        redundant: {description: ""}
-        missedIntrons: {description: ""}
+        stats: {description: "Various statistics related to the “accuracy” (or a measure of agreement) of the input transcripts when compared to reference annotation data."}
+        tracking: {description: "File matching transcripts up between samples."}
+        allFiles: {description: "A collection of all outputs files."}
+        redundant: {description: "File containing "duplicate"/"redundant" transcripts."}
+        missedIntrons: {description: "File denoting missed introns."}
     }
 
     meta {

gffread.wdl

@@ -80,5 +80,11 @@ task GffRead {
         filteredGffPath: {description: "The location the filtered GFF should be written to.", 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"}
+
+        # outputs
+        exonsFasta: {description: "Fasta file containing exons."}
+        CDSFasta: {description: "Fasta file containing CDS's."}
+        proteinFasta: {description: "Fasta file containing proteins."}
+        filteredGff: {description: "Filtered GFF file."}
     }
 }

gridss.wdl

@@ -81,5 +81,11 @@ task GRIDSS {
         jvmHeapSizeGb: {description: "The size of JVM heap for assembly and variant calling.",category: "advanced"}
         threads: {description: "The number of the threads to use.", 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"}
+
+        # outputs
+        vcf: {description: ""}
+        vcfIndex: {description: ""}
+        assembly: {description: ""}
+        assemblyIndex: {description: ""}
     }
 }