Processes


NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET	1
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT	12
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT	1
CRAM_QC_RECAL:SAMTOOLS_STATS	8
CRAM_QC_RECAL:MOSDEPTH	8
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP	8
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM	1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP	8
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	20
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC	4
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	4
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	4
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	4
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER	4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION	4
BAM_VARIANT_CALLING_GERMLINE_ALL:GERMLINE_CNV	4
BAM_VARIANT_CALLING_GERMLINE_ALL:BGZIPTABIX_GERMLINE_CNV	4
BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_ESTIMATE_SEX
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_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL	4
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR	4
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_FACETS:CONVERT_NORMAL_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_FACETS:CONVERT_TUMOR_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	4
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC	4
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	36
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	4
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	4	1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI	4
BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE	4
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	4
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	4
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV	4
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL	4
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT	4
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES	4
VCF_SOMATIC_SNV_INDEL:WHATSHAP	98
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS	4
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP	4
VCF_SOMATIC_SNV_INDEL:TABIX_VEP	4
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS	4
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO	4
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF	4
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL	4
BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ	4
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ	98
BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS	4
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC	4
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING	4
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF	4
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS	4
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD	4
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2	4
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER	4
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	4
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	4
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM	4
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT	4
BAM_CHIP_DETECTION:TABIX_GERMLINE	4
HARMONIZE_GERMLINE:BCFTOOLS_NORM	4
HARMONIZE_GERMLINE:BCFTOOLS_SORT	4
HARMONIZE_CHIP_PON:BCFTOOLS_NORM	1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT	1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE	4
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON	4
BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES	4
BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER	4
BAM_CHIP_DETECTION:SENTIEON_GENOTYPE	4	1
BAM_CHIP_DETECTION:TRANSFER_CALLER_AD	4
BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS	4
VCF_DECONFLICT_VARIANTS:DECONFLICT_VARIANTS	4
SAREK:GENERATE_CHIP_REPORT	4
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS	24
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT	24
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL	24
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY	24
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA	4
CRAM_HLATYPING_ALL:SEQTK_SAMPLE	4
FASTQ_HLATYPING_OPTITYPE:OPTITYPE	4
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE	4
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	24
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	24
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	24
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	24
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	24
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	24
VCF_ANNOTATE_MERGE:TABIX_TABIX	24
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	4
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	4
VCF_TMB:TMB	4
SAREK:AGGREGATE_VARIANT_QC	1
SAREK:VARIANT_QC_TO_CSV	1
SAREK:MULTIQC	1
SAREK:WRITE_TRACKER_YML	1