<commit_before><?xml version="1.1" encoding="ISO-8859-1"?>
<pipe:pipeline xmlns:pipe="http://cancerresearchuk.org/workflow/pipeline"
               xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
               xsi:schemaLocation="http://cancerresearchuk.org/workflow/pipeline http://content.cruk.cam.ac.uk/bioinformatics/schema/workflow/pipeline-1.6.xsd">

    <name>Multi-Genome Alignment Pipeline</name>
    <description>Contaminant screen for high-throughput sequencing data that aligns to multiple reference genomes and adapter sequences.</description>

    <defaultJobName>mga.${runId}${datasetId|.%}${chunkNumber|.%}${referenceGenomeId|.%}.${task}</defaultJobName>

    <metaDataStructure>
        <variable name="runId"/>
        <variable name="sampleSheetFile"/>
    </metaDataStructure>

    <defaultResources>
        <memory>512M</memory>
        <jvmOverhead>128M</jvmOverhead>
    </defaultResources>

    <variables>
        <work>@{user.dir}</work>
        <dataDir>${work}</dataDir>
        <outputDir>${work}</outputDir>
        <resourcesDir>${install}/resources</resourcesDir>
        <bowtieIndexDir>${resourcesDir}/bowtie_indexes</bowtieIndexDir>
        <adapterFastaFile>${resourcesDir}/adapters.fa</adapterFastaFile>
        <referenceGenomeMappingFile>${resourcesDir}/reference_genome_mappings.txt</referenceGenomeMappingFile>
        <xslStyleSheetFile>${install}/resources/results.xsl</xslStyleSheetFile>
        <bowtieExecutable>bowtie</bowtieExecutable>
        <exonerateExecutable>exonerate</exonerateExecutable>
        <sampleSize>100000</sampleSize>
        <maxNumberOfRecordsToSampleFrom>5000000</maxNumberOfRecordsToSampleFrom>
        <chunkSize>5000000</chunkSize>
        <trimLength>36</trimLength>
        <plotWidth>800</plotWidth>
        <minimumSequenceCount>10</minimumSequenceCount><commit_msg>Updated to workflow 1.7 schema.<commit_after><?xml version="1.1" encoding="ISO-8859-1"?>
<pipe:pipeline xmlns:pipe="http://cancerresearchuk.org/workflow/pipeline"
               xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
               xsi:schemaLocation="http://cancerresearchuk.org/workflow/pipeline http://content.cruk.cam.ac.uk/bioinformatics/schema/workflow/pipeline-1.7.xsd">

    <name>Multi-Genome Alignment Pipeline</name>
    <description>Contaminant screen for high-throughput sequencing data that aligns to multiple reference genomes and adapter sequences.</description>

    <defaultJobName>${runId}${datasetId|.%}${chunkNumber|.%}${referenceGenomeId|.%}.${task}</defaultJobName>

    <metaDataStructure>
        <variable name="runId"/>
        <variable name="sampleSheetFile"/>
    </metaDataStructure>

    <defaultResources>
        <memory>512M</memory>
        <jvmOverhead>128M</jvmOverhead>
    </defaultResources>

    <variables>
        <work>@{user.dir}</work>
        <dataDir>${work}</dataDir>
        <outputDir>${work}</outputDir>
        <resourcesDir>${install}/resources</resourcesDir>
        <bowtieIndexDir>${resourcesDir}/bowtie_indexes</bowtieIndexDir>
        <adapterFastaFile>${resourcesDir}/adapters.fa</adapterFastaFile>
        <referenceGenomeMappingFile>${resourcesDir}/reference_genome_mappings.txt</referenceGenomeMappingFile>
        <xslStyleSheetFile>${install}/resources/results.xsl</xslStyleSheetFile>
        <bowtieExecutable>bowtie</bowtieExecutable>
        <exonerateExecutable>exonerate</exonerateExecutable>
        <sampleSize>100000</sampleSize>
        <maxNumberOfRecordsToSampleFrom>5000000</maxNumberOfRecordsToSampleFrom>
        <chunkSize>5000000</chunkSize>
        <trimLength>36</trimLength>
        <plotWidth>800</plotWidth>
        <minimumSequenceCount>10</minimumSequenceCount>
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