add tasks for biowdl-input-converter

biowdl.wdl

+version 1.0
+
+# Copyright (c) 2018 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 InputConverter {
+    input {
+        File samplesheet
+        String outputFile = "samplesheet.json"
+        Boolean skipFileCheck=false
+        Boolean checkFileMd5sums=true
+        Boolean old=false
+    }
+
+    command <<<
+        biowdl-input-converter \
+        -o ~{outputFile} \
+        ~{true="--skip-file-check" false="" skipFileCheck} \
+        ~{true="--check-file-md5sums" false="" checkFileMd5sums} \
+        ~{true="--old" false="" old} \
+    >>>
+
+    output {
+        File json = outputFile
+    }
+
+    runtime {
+        docker: "quay.io/biocontainers/biowdl-input-converter:0.1.0--py_0"
+    }
+}