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WESIM, WholeGenomeGermlineSingleSample - Coggle Diagram

- - - - SampleAndUnmappedBams
      - GermlineSingleSampleReferences
      - PapiSettings
      - File
        
        contamination_sites_ud
        
        contamination_sites_bed
        
        contamination_sites_mu
        
        haplotype_database_file
    - - Alignment.GetBwaVersion
      - scatter
        
        sample_and_unmapped_bams.flowcell_unmapped_bams
        
        QC.CollectQualityYieldMetrics
        
        Alignment.SamToFastqAndBwaMemAndMba
        
        QC.CollectUnsortedReadgroupBamQualityMetrics
      - Utils.SumFloats
      - BamProcessing
        
        SortSam
        
        command {
        
        java -Dsamjdk.compression_level=~{compression_level} -Xms4000m -jar /usr/gitc/picard.jar \
        
        SortSam \
        
        INPUT=~{input_bam} \
        
        OUTPUT=~{output_bam_basename}.bam \
        
        SORT_ORDER="coordinate" \
        
        CREATE_INDEX=true \
        
        CREATE_MD5_FILE=true \
        
        MAX_RECORDS_IN_RAM=300000
        
        CheckContamination
        
        scatter
        
        CreateSequenceGroupingTSV.sequence_grouping
        
        BaseRecalibrator
        
        command {
        
        gatk --java-options "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal \
        
        10 more items...
        
        Processing.GatherBqsrReports
        
        command {
        
        gatk --java-options "-Xms3000m" \
        
        GatherBQSRReports \
        
        -I ~{sep=' -I ' input_bqsr_reports} \
        
        -O ~{output_report_filename}
        
        output
        
        output_bqsr_report
        
        scatter
        
        CreateSequenceGroupingTSV.sequence_grouping_with_unmapped
        
        ApplyBQSR
        
        command {
        
        gatk --java-options "-XX:+PrintFlagsFinal -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps \
        
        14 more items...
        
        input
        
        input_bam
        
        recalibration_report
        
        1 more item...
        
        output
        
        recalibrated_bam
        
        1 more item...
        
        GatherSortedBamFiles
        
        input
        
        input_bams
        
        ApplyBQSR.recalibrated_bam
        
        command {
        
        java -Dsamjdk.compression_level=~{compression_level} -Xms2000m -jar /usr/gitc/picard.jar \
        
        GatherBamFiles \
        
        INPUT=~{sep=' INPUT=' input_bams} \
        
        OUTPUT=~{output_bam_basename}.bam \
        
        CREATE_INDEX=true \
        
        CREATE_MD5_FILE=true
        
        output
        
        output_bam
        
        MarkDuplicates
        
        command {
        
        java -Dsamjdk.compression_level=~{compression_level} -Xms~{java_memory_size}g -jar /usr/gitc/picard.jar \
        
        MarkDuplicates \
        
        INPUT=~{sep=' INPUT=' input_bams} \
        
        OUTPUT=~{output_bam_basename}.bam \
        
        METRICS_FILE=~{metrics_filename} \
        
        VALIDATION_STRINGENCY=SILENT \
        
        ~{"READ_NAME_REGEX=" + read_name_regex} \
        
        OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
        
        ASSUME_SORT_ORDER="queryname" \
        
        CLEAR_DT="false" \
        
        ADD_PG_TAG_TO_READS=false
    - - output_bam
        
        GatherBamFiles.output_bam