diff --git a/TO-DO.md b/TO-DO.md
index 69f359bdf7d130a48eb06e938a84a7aa6b9b0ee2..7368005aed8a0527ca448c2731910c260866341e 100644
--- a/TO-DO.md
+++ b/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
diff --git a/deepvariant.wdl b/deepvariant.wdl
index 618200aa8df9c3b4be9700d323d48eaf300f5eb6..28aee813b170590aaf233b5fb912bff0d180b823 100644
--- a/deepvariant.wdl
+++ b/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"}
diff --git a/multiqc.wdl b/multiqc.wdl
index 1d248dd6a5922b0e414353bd323d3625a29140e7..405c0a0bbf36377c700f1bd00406a1183c64a5c0 100644
--- a/multiqc.wdl
+++ b/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."}
}
}
diff --git a/pacbio.wdl b/pacbio.wdl
index 01f6d4fdaff1d7ef933d7d981fea21bf8b025290..df0343d98a737132f82185a04bca133547137659 100644
--- a/pacbio.wdl
+++ b/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`."}
}
}
diff --git a/pbbam.wdl b/pbbam.wdl
index d271a11a6066135334def2202aeec2393f688324..d893e64d33ce6867695b8f48a36e8acb4aa0adc2 100644
--- a/pbbam.wdl
+++ b/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."}
}
}
diff --git a/picard.wdl b/picard.wdl
index f1876f7b6bd2849db7ef8b257e331a5fa7040ee9..d288f0e58cfe1743b112b6ee1220cc49a86744fa 100644
--- a/picard.wdl
+++ b/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: ""}
}
}