Commit 71426017 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added the -T arg

parent ce85fe0a
...@@ -27,10 +27,11 @@ class SamtoolsSort(val root: Configurable) extends Samtools { ...@@ -27,10 +27,11 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
prefix = config("prefix", default = new File(Files.createTempDir(), output.getAbsolutePath)) prefix = config("prefix", default = new File(Files.createTempDir(), output.getAbsolutePath))
} }
def cmdLine = executable + required("sort") + def cmdLine = required(executable) + required("sort") +
optional("-m", (coreMemeory + "G")) + optional("-m", (coreMemeory + "G")) +
optional("-@", threads) + optional("-@", threads) +
optional("-O", outputFormat) + optional("-O", outputFormat) +
required("-T", prefix) +
conditional(sortByName, "-n") + conditional(sortByName, "-n") +
(if (outputAsStsout) "" else required("-o", output)) + (if (outputAsStsout) "" else required("-o", output)) +
(if (inputAsStdin) "" else required(input)) (if (inputAsStdin) "" else required(input))
......
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