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Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction)

This commit is contained in:
Mauricio Carneiro 2011-07-16 00:09:00 -04:00
parent fd1df31ef0
commit ed55182a4c
1 changed files with 10 additions and 10 deletions
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20
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -3,10 +3,11 @@ package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.function.ListWriterFunction
import org.broadinstitute.sting.queue.extensions.picard._
import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode
import collection.JavaConversions._
import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
import org.broadinstitute.sting.queue.extensions.picard._
import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMFileHeader.SortOrder
@ -29,6 +30,11 @@ class DataProcessingPipeline extends QScript {
@Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true)
var reference: File = _
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
var dbSNP: File = _
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=true)
var indels: File = _
/****************************************************************************
@ -42,12 +48,6 @@ class DataProcessingPipeline extends QScript {
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
var projectName: String = "project"
@ -295,7 +295,7 @@ class DataProcessingPipeline extends QScript {
this.targetIntervals = tIntervals
this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.consensusDeterminationModel = consensusDeterminationModel
this.compress = 0
this.scatterCount = nContigs
@ -318,7 +318,7 @@ class DataProcessingPipeline extends QScript {
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
this.input_file :+= inBam
this.recal_file = inRecalFile
this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
this.baq = CalculationMode.CALCULATE_AS_NECESSARY
this.out = outBam
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals