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
111 58 35
CRAM_QC_RECAL:MOSDEPTH
169 11
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
169 13
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
AIH_CNV:ClusterPanelRegions
1
AIH_CNV:CalcPanelCoverage
52 2
AIH_CNV:ProcessBatch
AIH_CNV:ModelSingle
AIH_CNV:AggregateBatchData
AIH_CNV:MakeVCFsProbeMerge
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
52
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
52
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
52
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
52
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
107 153 60
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
3 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
1
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
52 9
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
260 20
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
52
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
52
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
52
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
260
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
52
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
52
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
157
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
157
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
152 4 6
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
126
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
107
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_MUTECT2:MUTECT2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
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
22
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
117 5
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
117
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
37 80 6
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
24 12
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
13
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
24 12
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
109 8
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
29 514
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
103 14 15
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso
117 3
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin
117 2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
1 584
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
110
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
378 207
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
22
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
26 10
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
14
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
3 114
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
3
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
69 191
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
260
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
52
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
52
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
1
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
1
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
1
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
1
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
1
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
309 14
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
309 14
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
309 14
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
309 14
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
52
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
52
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
169
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
22
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
309 14
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
278
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
230
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
152 15
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
79
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
25 5
VCF_ANNOTATE_MERGE:TABIX_TABIX
8
SAREK:TMB
SAREK:AGGREGATE_VARIANT_QC
SAREK:MULTIQC