Processes

NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT
48
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT
CRAM_QC_RECAL:SAMTOOLS_STATS
48
CRAM_QC_RECAL:MOSDEPTH
48
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
48
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
48
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
43 2
BAM_QC_SEX_ESTIMATION:BAM_ESTIMATE_SEX
48
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
25
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC
5
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
5
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
5
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
5
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER
5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION
5
BAM_VARIANT_CALLING_GERMLINE_ALL:GERMLINE_CNV
BAM_VARIANT_CALLING_GERMLINE_ALL:BGZIPTABIX_GERMLINE_CNV
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: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
49
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
49 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
49
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
49
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
49
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
49
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
441
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
49
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
49
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
49 1
BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE
49
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
49
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
49
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV
49
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL
49
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT
49
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES
49
VCF_SOMATIC_SNV_INDEL:WHATSHAP
1204
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS
49
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP
49
VCF_SOMATIC_SNV_INDEL:TABIX_VEP
49
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS
49
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO
49
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF
49
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL
49
BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ
49
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ
1205
BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS
49
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
49
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
49
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
49
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
49
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
5
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
5
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
5
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
5
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
5
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
5
BAM_CHIP_DETECTION:TABIX_GERMLINE
5
HARMONIZE_GERMLINE:BCFTOOLS_NORM
5
HARMONIZE_GERMLINE:BCFTOOLS_SORT
5
HARMONIZE_CHIP_PON:BCFTOOLS_NORM
1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT
1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE
5
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON
5
BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES
5
BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER
5
BAM_CHIP_DETECTION:SENTIEON_GENOTYPE
5 3
BAM_CHIP_DETECTION:TRANSFER_CALLER_AD
5
BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS
5
VCF_DECONFLICT_VARIANTS:DECONFLICT_VARIANTS
5
SAREK:GENERATE_CHIP_REPORT
5
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
201
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
201
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
201
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
201
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
5
CRAM_HLATYPING_ALL:SEQTK_SAMPLE
5
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
5
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
5
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
201
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
201
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
201
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
201
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
201
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
201
VCF_ANNOTATE_MERGE:TABIX_TABIX
201
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
49
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
49
VCF_TMB:TMB
49
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:VARIANT_QC_TO_CSV
1
SAREK:MULTIQC
1
SAREK:WRITE_TRACKER_YML
1