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cutadapt.wdl

@@ -237,17 +237,17 @@ task Cutadapt {
         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
-        cutRead1: {description: ""}
-        report: {description: ""}
-        cutRead2: {description: ""}
-        tooLongOutput: {description: ""}
-        tooShortOutput: {description: ""}
-        untrimmedOutput: {description: ""}
-        tooLongPairedOutput: {description: ""}
-        tooShortPairedOutput: {description: ""}
-        untrimmedPairedOutput: {description: ""}
-        infoFile: {description: ""}
-        restFile: {description: ""}
-        wildcardFile: {description: ""}
+        cutRead1: {description: "Trimmed read one."}
+        report: {description: "Per-adapter statistics file."}
+        cutRead2: {description: "Trimmed read two in pair."}
+        tooLongOutput: {description: "Reads that are too long according to -M."}
+        tooShortOutput: {description: "Reads that are too short according to -m."}
+        untrimmedOutput: {description: "All reads without adapters (instead of the regular output file)."}
+        tooLongPairedOutput: {description: "Second reads in a pair."}
+        tooShortPairedOutput: {description: "Second reads in a pair."}
+        untrimmedPairedOutput: {description: "The second reads in a pair that were not trimmed."}
+        infoFile: {description: "Detailed information about where adapters were found in each read."}
+        restFile: {description: "The rest file."}
+        wildcardFile: {description: "The wildcard file."}
     }
 }

deepvariant.wdl

@@ -90,5 +90,12 @@ task RunDeepVariant {
         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"}
+
+        # outputs
+        outputVCF: {description: "Output VCF file."}
+        outputVCFIndex: {description: "Index of output VCF file."}
+        outputVCFStatsReport: {description: "Statistics file."}
+        outputGVCF: {description: "GVCF version of VCF file(s)."}
+        outputGVCFIndex: {description: "Index of GVCF file(s)."}
     }
 }

delly.wdl

@@ -62,5 +62,8 @@ task CallSV {
         memory: {description: "The memory required to run the programs.", 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
+        dellyBcf: {description: "File containing structural variants."}
     }
 }

fastqc.wdl

@@ -125,6 +125,13 @@ task Fastqc {
         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"}
+
+        # outputs
+        htmlReport: {description: ""}
+        reportZip: {description: ""}
+        summary: {description: ""}
+        rawReport: {description: ""}
+        images: {description: ""}
     }
 
     meta {
@@ -167,5 +174,10 @@ task GetConfiguration {
         # inputs
         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
+        adapterList: {description: ""}
+        contaminantList: {description: ""}
+        limits: {description: ""}
     }
 }