Processes

PREPARE_GENOME:BWAMEM1_INDEX
PREPARE_GENOME:BWAMEM2_INDEX
PREPARE_GENOME:DRAGMAP_HASHTABLE
PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
PREPARE_GENOME:SAMTOOLS_FAIDX
PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS
PREPARE_GENOME:TABIX_DBSNP
PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
PREPARE_GENOME:TABIX_KNOWN_SNPS
PREPARE_GENOME:TABIX_KNOWN_INDELS
PREPARE_GENOME:TABIX_PON
PREPARE_GENOME:UNZIP_ALLELES
PREPARE_GENOME:UNZIP_LOCI
PREPARE_GENOME:UNZIP_GC
PREPARE_GENOME:UNZIP_RT
PREPARE_GENOME:UNTAR_CHR_DIR
PREPARE_GENOME:YARA_HLA_INDEX
PREPARE_INTERVALS:BUILD_INTERVALS
PREPARE_INTERVALS:CREATE_INTERVALS_BED
1
PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
5
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
1
PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET
1
PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE
1
NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_QC_RECAL:SAMTOOLS_STATS
23 151 11
CRAM_QC_RECAL:MOSDEPTH
54 118 12
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
56 117 12
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
AIH_CNV:ClusterPanelRegions
1
AIH_CNV:CalcPanelCoverage
3 51 5
AIH_CNV:ProcessBatch
AIH_CNV:ModelSingle
AIH_CNV:AggregateBatchData
AIH_CNV:MakeVCFsProbeMerge
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
44 10
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
14 30
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
3 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
14 30
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
12 254 9
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
2
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
2
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
3 48 5
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
207 52 13
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
250 9 11
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
3
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
3
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
3
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_TUMOR_ONLY_ALL:BAM_ESTIMATE_SEX
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2
15
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES
15
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
3
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
3
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY
3 3
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL
22
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
105 9 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
81
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
84
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
79
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
82
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso
80
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin
88
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
422
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
12 98
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
1 409
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
83
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2
12 258
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES
84 186
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
1 1
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
VCF_ANNOTATE_MERGE:TABIX_TABIX
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
BAM_CHIP_DETECTION:TABIX_GERMLINE
BAM_CHIP_DETECTION:TABIX_SOMATIC
HARMONIZE_GERMLINE:BCFTOOLS_NORM
HARMONIZE_GERMLINE:BCFTOOLS_SORT
HARMONIZE_SOMATIC:BCFTOOLS_NORM
HARMONIZE_SOMATIC:BCFTOOLS_SORT
HARMONIZE_CHIP_PON:BCFTOOLS_NORM
1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT
1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
3
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
3
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
3
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
3
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
51 3 1
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
1 49 2
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
95 76 9
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
14
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
3
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
VCF_ANNOTATE_MERGE:TABIX_TABIX
SAREK:TMB
SAREK:AGGREGATE_VARIANT_QC
SAREK:MULTIQC