Merge pull request #112 from biowdl/KG-295

Add CNV callers

LICENSE

 MIT License
 
-Copyright (c) 2018 Leiden University Medical Center
+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

bedtools.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 inputBed
+        Boolean sizeA = false
+        Boolean sizeD = false
+        Boolean chrThenSizeA = false
+        Boolean chrThenSizeD = false
+        Boolean chrThenScoreD = false
+        File? g
+        File? faidx
+        Boolean header = false
+        String outputBed = "output.sorted.bed"
+        String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputBed})
+        bedtools sort \
+        -i ~{inputBed} \
+        ~{if sizeA then "-sizeA" else ""} \
+        ~{if sizeD then "-sizeD" else ""} \
+        ~{if chrThenSizeD then "-chrThenSizeD" else ""} \
+        > ~{outputBed}
+    }
+
+    output {
+        File bedFile = outputBed
+    }
+
+    runtime {
+        docker: dockerImage
+    }
+
+
+}
\ No newline at end of file

wisestork.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 Count {
+    input {
+        Int? binSize
+        File reference
+        File referenceIndex
+        File? binFile
+        File inputBam
+        File inputBamIndex
+        String outputBed = "output.bed"
+        String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputBed})
+        wisestork count \
+        ~{"--binsize " + binSize} \
+       --reference ~{reference} \
+       ~{"--bin-file " + binFile} \
+       --output ~{outputBed} \
+       --input ~{inputBam}
+    }
+
+    output {
+        File bedFile = outputBed
+    }
+
+    runtime {
+        docker: dockerImage
+    }
+}
+
+task GcCorrect {
+    input {
+        Int? binSize
+        File reference
+        File referenceIndex
+        File? binFile
+        File inputBed
+        String outputBed = "output.bed"
+        Float? fracN
+        Int? iter
+        Float? fracLowess
+        String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputBed})
+        wisestork gc-correct \
+        ~{"--binsize " + binSize} \
+        --reference ~{reference} \
+        ~{"--bin-file " + binFile} \
+        --output ~{outputBed} \
+        --input ~{inputBed} \
+        ~{"--frac-n " + fracN} \
+        ~{"--iter " + iter} \
+        ~{"--frac-lowess " + fracLowess}
+    }
+
+    output {
+        File bedFile = outputBed
+    }
+
+    runtime {
+        docker: dockerImage
+    }
+}
+
+task Newref {
+    input {
+        Int? binSize
+        File reference
+        File referenceIndex
+        File? binFile
+        Array[File]+ inputBeds
+        String outputBed = "output.bed"
+        Int? nBins
+        String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputBed})
+        wisestork newref \
+        ~{"--binsize " + binSize} \
+       --reference ~{reference} \
+       ~{"--bin-file " + binFile} \
+       --output ~{outputBed} \
+       -I ~{sep=" -I " inputBeds} \
+       ~{"--n-bins " + nBins}
+    }
+
+    output {
+        File bedFile = outputBed
+    }
+
+    runtime {
+        docker: dockerImage
+        memory: 2 + ceil(length(inputBeds) * 0.15)
+    }
+}
+
+task Zscore {
+    input {
+        Int? binSize
+        File reference
+        File referenceIndex
+        File? binFile
+        File inputBed
+        File inputBedIndex
+        File dictionaryFile
+        File dictionaryFileIndex
+        String outputBed = "output.bed"
+        String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputBed})
+        wisestork zscore \
+        ~{"--binsize " + binSize} \
+        --reference ~{reference} \
+        ~{"--bin-file " + binFile} \
+        --output ~{outputBed} \
+        --input ~{inputBed} \
+        ~{"--dictionary-file " + dictionaryFile}
+    }
+
+    output {
+        File bedFile = outputBed
+    }
+
+    runtime {
+        docker: dockerImage
+    }
+}
+