From 31b21e1e197b5c646b2ad202cd4fa56cc54816e8 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Fri, 14 Aug 2020 16:10:47 +0200
Subject: [PATCH] add bcftools annotate
---
bcftools.wdl | 100 +++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 100 insertions(+)
diff --git a/bcftools.wdl b/bcftools.wdl
index 8875903..33685c3 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -22,6 +22,106 @@ version 1.0
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
+task Annotate {
+ input {
+ File? annsFile
+ String? collapse
+ Array[String] columns = []
+ String? exclude
+ Boolean force = false
+ File? headerLines
+ String? newId
+ String? include
+ Boolean keepSites = false
+ String? markSites
+ Boolean noVersion = false
+ String outputType = "z"
+ String? regions
+ File? regionsFile
+ File? renameChrs
+ Array[String] samples = []
+ File? samplesFile
+ Boolean singleOverlaps = false
+ Array[String] removeAnns = []
+ File inputFile
+ String outputPath = "output.vcf.gz"
+
+ Int threads = 0
+ String memory = "256M"
+ Int timeMinutes = 1 + ceil(size(inputFile, "G"))
+ String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ bcftools annotate \
+ -o ~{outputPath} \
+ -O ~{outputType} \
+ ~{"--annotations " + annsFile} \
+ ~{"--collapse " + collapse} \
+ ~{true="--columns" false="" length(columns) > 0} ~{sep="," columns} \
+ ~{"--exclude " + exclude} \
+ ~{true="--force" false="" force} \
+ ~{"--header-lines " + headerLines} \
+ ~{"--set-id " + newId} \
+ ~{"--include " + include} \
+ ~{true="--keep-sites" false="" keepSites} \
+ ~{"--mark-sites " + markSites} \
+ ~{true="--no-version" false="" noVersion} \
+ ~{"--regions " + regions} \
+ ~{"--regions-file " + regionsFile} \
+ ~{"--rename-chrs " + renameChrs} \
+ ~{true="--samples" false="" length(samples) > 0} ~{sep="," samples} \
+ ~{"--samples-file " + samplesFile} \
+ ~{true="--single-overlaps" false="" singleOverlaps} \
+ ~{true="--remove" false="" length(removeAnns) > 0} ~{sep="," removeAnns} \
+ ~{inputFile}
+ bcftools index --tbi ~{outputPath}
+
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ outputType: {description: "Output type: v=vcf, z=vcf.gz, b=bcf, u=uncompressed bcf", category: "advanced"}
+ annsFile: {description: "Bgzip-compressed and tabix-indexed file with annotations (see man page for details).", category: "advanced"}
+ collapse: {description: "Treat as identical records with <snps|indels|both|all|some|none>, see man page for details.", category: "advanced"}
+ columns: {description: "Comma-separated list of columns or tags to carry over from the annotation file (see man page for details).", category: "advanced"}
+ exclude: {description: "Exclude sites for which the expression is true (see man page for details).", category: "advanced"}
+ force: {description: "Continue even when parsing errors, such as undefined tags, are encountered.", category: "advanced"}
+ headerLines: {description: "Lines to append to the VCF header (see man page for details).", category: "advanced"}
+ newId: {description: "Assign ID on the fly (e.g. --set-id +'%CHROM\_%POS').", category: "advanced"}
+ include: {description: "Select sites for which the expression is true (see man page for details).", category: "advanced"}
+ keepSites: {description: "Keep sites which do not pass -i and -e expressions instead of discarding them.", category: "advanced"}
+ markSites: {description: "Annotate sites which are present ('+') or absent ('-') in the -a file with a new INFO/TAG flag.", category: "advanced"}
+ noVersion: {description: "Do not append version and command line information to the output VCF header.", category: "advanced"}
+ regions: {description: "Restrict to comma-separated list of regions.", category: "advanced"}
+ regionsFile: {description: "Restrict to regions listed in a file.", category: "advanced"}
+ renameChrs: {description: "rename chromosomes according to the map in file (see man page for details).", category: "advanced"}
+ samples: {description: "List of samples for sample stats, \"-\" to include all samples.", category: "advanced"}
+ samplesFile: {description: "File of samples to include.", category: "advanced"}
+ singleOverlaps: {description: "keep memory requirements low with very large annotation files.", category: "advanced"}
+ removeAnns: {description: "List of annotations to remove (see man page for details).", category: "advanced"}
+ inputFile: {description: "A vcf or bcf file.", category: "required"}
+
+ threads: {description: "Number of extra decompression threads [0].", 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"}
+ 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"}
+ }
+}
+
task View {
input {
File inputFile
--
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