diff --git a/LICENSE b/LICENSE index e580f6d99dbca59917e53a3ef91afb0991bcd0f5..37eeade523725cb9bd806d9a110674c56d7bb80e 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ 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 diff --git a/bedtools.wdl b/bedtools.wdl new file mode 100644 index 0000000000000000000000000000000000000000..acc8132c8c066f248a786e774ef62d146ceff176 --- /dev/null +++ b/bedtools.wdl @@ -0,0 +1,58 @@ +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 diff --git a/wiseguy.wdl b/wiseguy.wdl index 5accca5189aabef4189836d385bfafa24b58290c..c5e8b17b8d621d102bcdc7c62f3e33cfd570e879 100644 --- a/wiseguy.wdl +++ b/wiseguy.wdl @@ -1,6 +1,6 @@ version 1.0 -# 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