Add more updates.

TO-DO.md

@@ -18,6 +18,8 @@ Some tasks are importing other WDL files.
 * fastqsplitter.wdl: `Fastqsplitter`
 * flash.wdl: `Flash`
 * macs2.wdl: `PeakCalling`
+* ncbi.wdl: `GenomeDownload`, `DownloadNtFasta`, `DownloadAccessionToTaxId`
+* 
 
 ## Imports other tasks:
 * bamstats.wdl

deepvariant.wdl

@@ -44,7 +44,6 @@ task RunDeepVariant {
 
     command {
         set -e
-
         /opt/deepvariant/bin/run_deepvariant \
         --ref ~{referenceFasta} \
         --reads ~{inputBam} \
@@ -85,7 +84,7 @@ task RunDeepVariant {
         customizedModel: {description: "A path to a model checkpoint to load for the `call_variants` step. If not set, the default for each --model_type will be used.", category: "advanced"}
         numShards: {description: "Number of shards for make_examples step.", category: "common"}
         outputGVcf: {description: "Path where we should write gVCF file.", category: "common"}
-        outputGVcfIndex: {description: "Path to where the gVCF index file will be written. This is needed as a workaround, set it to outputGVcf+.tbi.", category: "common"}
+        outputGVcfIndex: {description: "Path to where the gVCF index file will be written. This is needed as a workaround, set it to `outputGVcf + '.tbi.'`", category: "common"}
         regions: {description: "List of regions we want to process, in BED/BEDPE format.", category: "advanced"}
         sampleName: {description: "Sample name to use instead of the sample name from the input reads BAM (SM tag in the header).", category: "common"}
         VCFStatsReport: {description: "Output a visual report (HTML) of statistics about the output VCF.", category: "common"}

multiqc.wdl

@@ -179,7 +179,7 @@ task MultiQC {
         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
-        multiqcReport: {description: ""}
-        multiqcDataDirZip: {description: ""}
+        multiqcReport: {description: "Results from bioinformatics analyses across many samples in a single report."}
+        multiqcDataDirZip: {description: "The parsed data directory compressed with zip."}
     }
 }

pacbio.wdl

@@ -43,7 +43,7 @@ task mergePacBio {
     }
 
     output {
-        File MergedReport = mergedReport
+        File outputMergedReport = mergedReport
     }
 
     parameter_meta {
@@ -52,6 +52,9 @@ task mergePacBio {
         mergedReport: {description: "The location the merged PacBio report file should be written to.", category: "common"}
         memory: {description: "The amount of memory this job will 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
+        outputMergedReport: {description: "The PacBio reports merged into one."}
     }
 }
 
@@ -85,5 +88,8 @@ task ccsChunks {
         chunkCount: {description: "The number of chunks to create.", category: "required"}
         memory: {description: "The amount of memory this job will 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
+        chunks: {description: "The chunks created based on `chunkCount`."}
     }
 }

pbbam.wdl

@@ -66,5 +66,9 @@ task Index {
         memory: {description: "The amount of memory needed for the job.", 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
+        indexedBam: {description: "The original input BAM file."}
+        index: {description: "The index of the input BAM file."}
     }
 }

picard.wdl

@@ -61,6 +61,9 @@ task BedToIntervalList {
         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
+        intervalList: {description: "Picard Interval List from a BED file."}
     }
 }
 
@@ -125,6 +128,9 @@ task CollectHsMetrics {
         memoryMb: {description: "The amount of memory this job will use in megabytes.", 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
+        HsMetrics: {description: "Hybrid-selection (HS) metrics for the input BAM file."}
     }
 }
 
@@ -240,6 +246,9 @@ task CollectMultipleMetrics {
         memoryMb: {description: "The amount of memory this job will use in megabytes.", 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
+        alignmentSummary: {description: ""}
     }
 }