add license notice to snpeff, add index input for bcftools annotate, and BWA...

add license notice to snpeff, add index input for bcftools annotate, and BWA mem index image input for gridss annotate inserted sequences

bcftools.wdl

@@ -44,6 +44,7 @@ task Annotate {
         Boolean singleOverlaps = false
         Array[String] removeAnns = []
         File inputFile
+        File? inputFileIndex
         String outputPath = "output.vcf.gz"
         
         Int threads = 0
@@ -117,6 +118,7 @@ task Annotate {
         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"}
+        ipnutFileIndex: {description: "The index for the input vcf or bcf.", "common"}
 
         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"}

gridss.wdl

@@ -93,6 +93,7 @@ task AnnotateInsertedSequence {
         File viralReference
         File viralReferenceFai
         File viralReferenceDict
+        File viralReferenceImg
 
         Int threads = 8
         String javaXmx = "8G"
@@ -134,6 +135,9 @@ task AnnotateInsertedSequence {
         inputVcf: {description: "The input VCF file.", category: "required"}
         outputPath: {description: "The path the output will be written to.", category: "common"}
         viralReference: {description: "A fasta file with viral sequences.", category: "required"}
+        viralReferenceFai: {description: "The index for the viral reference fasta.", category: "required"}
+        viralReferenceDict: {description: "The dict file for the viral reference.", category: "required"}
+        viralReferenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the viral reference.", category: "required"}
 
         memory: {description: "The amount of memory this job will use.", category: "advanced"}
         javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",

snpeff.wdl

 version 1.0
 
+# MIT License
+#
+# Copyright (c) 2020 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 SnpEff {
     input {
         File vcf