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Changed @Input to @Argument for non-File types

This commit is contained in:
Menachem Fromer 2012-10-26 01:21:05 -04:00
parent e0fa7d1497
commit 9af4b34fd8
1 changed files with 8 additions and 8 deletions
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16
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala
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@ -33,30 +33,30 @@ class xhmmCNVpipeline extends QScript {
@Argument(shortName = "L", doc = "Intervals", required = false)
var intervals: File = _
@Input(doc = "level of parallelism for BAM DoC. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
@Argument(doc = "level of parallelism for BAM DoC. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
var scatterCountInput = 0
@Input(doc = "Samples to run together for DoC. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false)
@Argument(doc = "Samples to run together for DoC. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false)
var samplesPerJob = 1
@Output(doc = "Base name for files to output", shortName = "o", required = true)
var outputBase: File = _
@Input(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false)
@Argument(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false)
var MAX_DEPTH = 20000
@Hidden
@Input(doc = "Number of read-depth bins", shortName = "NUM_BINS", required = false)
@Argument(doc = "Number of read-depth bins", shortName = "NUM_BINS", required = false)
var NUM_BINS = 200
@Hidden
@Input(doc = "Starting value of read-depth bins", shortName = "START_BIN", required = false)
@Argument(doc = "Starting value of read-depth bins", shortName = "START_BIN", required = false)
var START_BIN = 1
@Input(doc = "Minimum read mapping quality", shortName = "MMQ", required = false)
@Argument(doc = "Minimum read mapping quality", shortName = "MMQ", required = false)
var minMappingQuality = 0
@Input(doc = "Memory (in GB) required for storing the whole matrix in memory", shortName = "wholeMatrixMemory", required = false)
@Argument(doc = "Memory (in GB) required for storing the whole matrix in memory", shortName = "wholeMatrixMemory", required = false)
var wholeMatrixMemory = -1
@Argument(shortName = "minTargGC", doc = "Exclude all targets with GC content less than this value", required = false)
@ -496,4 +496,4 @@ class xhmmCNVpipeline extends QScript {
override def description = "Genotypes discovered CNVs (and their sub-segments, of up to " + maxTargetsInSubsegment + " targets) in all samples: " + command
}
}
}