Processes

BCL_TO_FASTQ:BCLCONVERT
8
DAQ:FLOWCELL_QC
DAQ:CAT_FASTQ
FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ
FASTQ_NGSCHECKMATE:NGSCHECKMATE_VAFNCM
DAQ:ESTIMATEGENDER
DAQ:MERGE_GENDER
DAQ:FASTP
DAQ:SENTIEON_BWAMEM
DAQ:SAMTOOLS_MERGE
DAQ:MARKDUPLICATES_SENTIEON
BAM_POSTDEDUP_QC:SAMTOOLS_STATS
BAM_POSTDEDUP_QC:MOSDEPTH
BAM_POSTDEDUP_QC:SENTIEON_MULTIPLE_METRICS
BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS
BAM_POSTDEDUP_QC:SEQTOOL
SENTIEON_BQSR:QUALCAL_TABLE
SENTIEON_BQSR:QUALCAL_APPLY
DAQ:AGGREGATE_POSTDEDUP_QC
DAQ:QC_JSON_TO_CSV
DAQ:MULTIQC
DAQ:WRITE_TRACKER_YML
DAQ:GENERATE_RESULTS_CSV
PREPARE_INTERVALS:BUILD_INTERVALS
PREPARE_INTERVALS:CREATE_INTERVALS_BED
1 1
PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ