Fix sambamba index command in sort

sambamba.wdl

+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 Sort {
+    input {
+        File inputBam
+        String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
+        Boolean sortByName = false
+        Int compressionLevel = 1
+        Int threads = 1
+        Int memoryPerThreadGb = 4
+        Int memoryGb = 1 + (threads + 1) * memoryPerThreadGb
+        String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
+        Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
+    }
+
+    # Select first needed as outputPath is optional input. (bug in cromwell)
+    String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
+
+    command {
+        set -e
+        mkdir -p "$(dirname ~{outputPath})"
+        sambamba sort \
+        -l ~{compressionLevel} \
+        ~{true="-n" false="" sortByName} \
+        ~{"--nthreads " + threads} \
+        -m ~{memoryPerThreadGb}G \
+        -o ~{outputPath} \
+        ~{inputBam}
+        sambamba index \
+        ~{"--nthreads " + threads} \
+         ~{outputPath} ~{bamIndexPath}
+    }
+
+    output {
+        File outputBam = outputPath
+        File outputBamIndex = bamIndexPath
+    }
+
+    runtime {
+        cpu: threads
+        memory: "~{memoryGb}G"
+        docker: dockerImage
+        time_minutes: timeMinutes
+    }
+
+    parameter_meta {
+        # inputs
+        inputBam: {description: "The input SAM file.", category: "required"}
+        outputPath: {description: "Output directory path + output file.", category: "required"}
+        sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
+        compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
+        memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
+        memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes", 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"}
+        threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
+        timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+        # outputs
+        outputBam: {description: "Sorted BAM file."}
+    }
+}
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