add tasks to create input files for DGE analysis

prepareShiny.wdl

+version 1.0
+
+# Copyright (c) 2017 Sequencing Analysis Support Core - 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 CreateDesignMatrix {
+    input {
+        File countTable
+        String shinyDir = "."
+
+        Int threads = 1
+        String memory = "5G"
+        Int timeMinutes = 30
+        String dockerImage = "quay.io/biocontainers/predex:0.9.1--pyh3252c3a_0"
+    }
+
+    command {
+        set -e
+        mkdir -p ${shinyDir}
+        predex design \
+            -i ${countTable} \
+            -o ${shinyDir}
+    }
+
+    output {
+        File dgeDesign = shinyDir + "/design_matrix.tsv"
+    }
+
+    runtime {
+        cpu: threads
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        countTable: {description: "The created count table from HTseq.", category: "required"}
+        shinyDir: {description: "The directory to write the output to.", category: "required"}
+        
+        threads: {description: "The number of threads to use.", 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"}
+    }
+}
+
+task CreateAnnotation {
+    input {
+        File referenceFasta
+        File referenceGtfFile
+        String shinyDir = "."
+
+        Int threads = 1
+        String memory = "10G"
+        Int timeMinutes = 90
+        String dockerImage = "quay.io/biocontainers/predex:0.9.1--pyh3252c3a_0"
+    }
+
+    command {
+        set -e
+        mkdir -p ${shinyDir}
+        predex annotation \
+            -f ${referenceFasta} \
+            -g ${referenceGtfFile} \
+            -o ${shinyDir}
+    }
+
+    output {        
+        File dgeAnnotation = shinyDir + "/annotation.tsv"
+    }
+
+    runtime {
+        cpu: threads
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        referenceFasta: {description: "The reference Fasta file.", category: "required"}
+        referenceGtfFile: {description: "The reference GTF file.", category: "required"}
+        shinyDir: {description: "The directory to write the output to.", category: "required"}
+        
+        threads: {description: "The number of threads to use.", 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"}
+    }
+}