Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity:
-- Picard extension so Queue scripts can use FastqToSam -- Single-sample BAM processing: merge/trim reads + BWA + IR + MD + BQSR. Mostly identical to standard pipeline, except for the adaptor trimming/merging which is critical for short-insert libraries. -- Single-sample calling (experimental, work in progress): standard UG run but outputting at all sites, meant for deep whole genomes. New scripts
This commit is contained in:
Guillermo del Angel
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.queue.extensions.picard
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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import org.broadinstitute.sting.commandline._
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import java.io.File
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class FastqToSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction /*with PicardBamFunction*/ {
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analysisName = "FastqToSam"
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javaMainClass = "net.sf.picard.sam.FastqToSam"
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@Input(shortName = "fq1", fullName = "input_fq_file1", required = true, doc = "Input Fastq file to extract reads from (single-end fastq or, if paired, first end of the pair fastq)")
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var fastq: File = _
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@Input(shortName = "fq2", fullName = "input_fq_file2", required = false, doc = "Input Fastq file to extract reads from (if paired, second end of the pair fastq).")
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var secondEndFastQ: File = _
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@Output(shortName = "bam", fullName = "output_bam_file", required = true, doc = "Output bam file .")
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var bam: File = _
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@Argument(shortName = "SM", fullName = "SM", required = false, doc = "SM")
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var SM: String = "SM"
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@Argument(shortName = "LIB", fullName = "LIB", required = false, doc = "LIB")
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var LIB: String = "LIB"
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@Argument(shortName = "PU", fullName = "PU", required = false, doc = "PU")
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var PU: String = "PU"
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@Argument(shortName = "RG", fullName = "RG", required = false, doc = "RG")
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var RG: String = "RG"
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@Argument(shortName = "PL", fullName = "PL", required = false, doc = "PL")
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var PL: String = "illumina"
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@Argument(shortName = "CN", fullName = "CN", required = false, doc = "CN")
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var CN: String = "CN"
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// override def inputBams = Seq(fastq)
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// override def outputBam = bam
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// this.sortOrder = null
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val createIndex:Boolean = true
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override def commandLine = super.commandLine +
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required("FASTQ=" + fastq) +
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optional("FASTQ2=", secondEndFastQ, spaceSeparated=false) +
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required("OUTPUT=" + bam) +
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optional("READ_GROUP_NAME=", RG, spaceSeparated=false) +
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required("SAMPLE_NAME=" + SM) +
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optional("LIBRARY_NAME=", LIB, spaceSeparated=false) +
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optional("PLATFORM_UNIT=", PU, spaceSeparated=false) +
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optional("PLATFORM=", PL, spaceSeparated=false) +
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optional("CREATE_INDEX=", createIndex, spaceSeparated=false) +
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optional("SEQUENCING_CENTER=", CN, spaceSeparated=false)
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}
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