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
50 2
CRAM_QC_RECAL:MOSDEPTH
50
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
50
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
AIH_CNV:ClusterPanelRegions
1
AIH_CNV:CalcPanelCoverage
25
AIH_CNV:ProcessBatch
1
AIH_CNV:ModelSingle
2657 4
AIH_CNV:AggregateBatchData
1
AIH_CNV:MakeVCFsProbeMerge
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
25
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
125 16
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
25
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
25
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
25
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
25 4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
125 6
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
25
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
25
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
25
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
125
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
25
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
25
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
100
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
100
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
100
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
100
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
100
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
25
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
25 1
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
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
25 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
25
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
25
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
25
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
125
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
25
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
25
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
25 2
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso
25 1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin
25 2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
125
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2
25
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS
25
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL
25
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL
125
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
125
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
25
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
25
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
25
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
25
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
25
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
25
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ
25 1
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
25
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
25
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF
25
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
25
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
25
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2
125
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
25
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
25
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
25
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES
125
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
25
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
25
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
25
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
25
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
25
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
25
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
25
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
25
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
25
VCF_ANNOTATE_MERGE:TABIX_TABIX
25
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY
25
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD
25
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR
25
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS
25
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
25
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
25
BAM_CHIP_DETECTION:TABIX_GERMLINE
25
BAM_CHIP_DETECTION:TABIX_SOMATIC
25
HARMONIZE_GERMLINE:BCFTOOLS_NORM
25
HARMONIZE_GERMLINE:BCFTOOLS_SORT
25
HARMONIZE_SOMATIC:BCFTOOLS_NORM
25
HARMONIZE_SOMATIC:BCFTOOLS_SORT
25
HARMONIZE_CHIP_PON:BCFTOOLS_NORM
1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT
1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE
25
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC
25
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON
25
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
275
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
275
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
275
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
275
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
25
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
25
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
25
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
50
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
25
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
275
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
275
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
275
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
275
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
275
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
275
VCF_ANNOTATE_MERGE:TABIX_TABIX
275
SAREK:TMB
25
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:MULTIQC
1