biowdl · rhpvorderman · Mar 5, 2025 · Feb 18, 2025 · Feb 19, 2025 · Feb 19, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
 
 version 6.0.0-dev
 ---------------------------
++ Add VEP task.
 + Add Sequali task.
 + Add Clair3 task.
 + Add Modkit task.

diff --git a/minimap2.wdl b/minimap2.wdl
@@ -183,6 +183,11 @@ task Mapping {
         mismatchPenalty: {description: "Mismatch penalty.", category: "advanced"}
         tagsToKeep: {description: "Tags to keep from the input unaligned BAM file.", category: "Advanced"}
         howToFindGTAG: {description: "How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG.", category: "common"}
+        compressionLevel: {description: "compressionLevel for the output file", category: "advanced"}
+        additionalSortThreads: {description: "Extra sorting threads used for samtools sort", category: "advanced"}
+        sortMemoryGb: {description: "Amount of memory set for sorting", category: "advanced"}
+        nameSorted: {description: "Output a name sorted file instead", category: "common"}
+
         cores: {description: "The number of cores to be used.", category: "advanced"}
         memory: {description: "The amount of memory available to the job.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}

diff --git a/vep.wdl b/vep.wdl
@@ -0,0 +1,110 @@
+version 1.0
+
+# Copyright (c) 2017 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Vep {
+    input {
+        File inputFile
+        String outputPath = "vep.annotated.vcf.gz"
+        File cacheTar
+        File? pluginsTar
+        String? species 
+        Array[String] plugins = []
+        Boolean refseq = false 
+        Boolean merged = false
+
+        Boolean everything = false
+        Boolean symbol = false
+
+        String memory = "8GiB"
+        # Account time for unpacking the cache.
+        Int timeMinutes = 1 + ceil(size(cacheTar, "GiB")) + ceil(size(inputFile, "MiB") * 3)
+        String dockerImage = "quay.io/biocontainers/ensembl-vep:113.3--pl5321h2a3209d_0"
+    }
+
+    command <<< 
+        set -eu
+        mkdir vep_cache
+        mkdir -p "$(dirname ~{outputPath})"
+        tar -x --directory vep_cache -f ~{cacheTar}
+        ~{"tar -x --directory vep_cache -f " + pluginsTar}
+
+        # Make sure vep can error, so the removal always succeeds.
+        set +e 
+        # Output all stats files by default for MultiQC integration
+        vep \
+        --input_file ~{inputFile} \
+        --output_file ~{outputPath} \
+        ~{"--species " + species} \
+        --stats_html --stats_text \
+        --dir vep_cache \
+        --offline \
+        ~{true="--plugin" false="" length(plugins) > 0} ~{sep=" --plugin " plugins} \
+        --vcf \
+        --compress_output bgzip \
+        ~{true="--refseq" false="" refseq} \
+        ~{true="--merged" false="" merged} \
+        ~{true="--everything" false="" everything} \
+        ~{true="--symbol" false="" symbol} 
+
+        VEP_EXIT_CODE=$?
+        set -e
+        # Cleanup the tar extract to save filesystem space
+        rm -rf vep_cache
+
+        exit $VEP_EXIT_CODE
+    >>>
+
+    output {
+        File outputFile = outputPath
+        File statsHtml = outputPath + "_summary.html"
+        File statsTxt = outputPath + "_summary.txt"
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+         # input
+        inputFile: {description: "The VCF to annotate.", category: "required"}
+        outputPath: {description: "Where to put the output file", category: "advanced"}
+        cacheTar: {description: "A TAR archive containing the cache. The TAR archives from the VEP website work.", category: "required"}
+        pluginsTar: {description: "A TAR file with custom plugins.", category: "advanced"}
+        species: {description: "Which species cache to use", category: "common"}
+        plugins: {description: "Which plugins to use", category: "common"}
+        refseq: {description: "Use the refseq cache", category: "common"}
+        merged: {description: "Use the merged cache", category: "common"}
+        everything: {description: "Use all annotation sources bundeld with vep.", category: "common"}
+        symbol: {description: "Add the gene symbol to the output where available", 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"}
+        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"}
+
+        # output
+        outputFile: {description: "The annotated VEP VCF file."}
+        statsHtml: {description: "The VEP summary stats HTML file."}
+        statsTxt: {description: "The VEP summary stats TXT file."}
+    }
+}