Processes

PREPARE_GENOME:BWAMEM1_INDEX
PREPARE_GENOME:BWAMEM2_INDEX
PREPARE_GENOME:DRAGMAP_HASHTABLE
PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
PREPARE_GENOME:MSISENSORPRO_SCAN
1 1
PREPARE_GENOME:MSISENSOR2_SCAN
1 1
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
1 1
PREPARE_GENOME:UNZIP_LOCI
1 1
PREPARE_GENOME:UNZIP_GC
1 1
PREPARE_GENOME:UNZIP_RT
1 1
PREPARE_GENOME:UNTAR_CHR_DIR
PREPARE_GENOME:YARA_HLA_INDEX
PREPARE_INTERVALS:BUILD_INTERVALS
PREPARE_INTERVALS:CREATE_INTERVALS_BED
1 1 1
PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
80 80 4
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
1 1 1
PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET
1 1 1
PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE
1 1 1
NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1 1
BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
160 8
BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
2 2
BAM_APPLYBQSR:GATK4_APPLYBQSR
160 8
CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
2 2
CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
2 2
SAREK:CRAM_TO_BAM_RECAL
2
CRAM_QC_RECAL:SAMTOOLS_STATS
2 2 2
CRAM_QC_RECAL:MOSDEPTH
2 2 2
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
2 2
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
1 1 1
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
80 80 80
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
1 1 1
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
1 1 1
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
1 1 1
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
1 1 1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
80 80 80
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
1 1 1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
1 1 1
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
1 1 1
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
80 80
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
1 1
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
1 1
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TIDDIT_SV
1 1
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TABIX_BGZIP_TIDDIT_SV
1 1
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
5 3 5
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
5 3 5
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
5 3 5
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
5 3 5
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
5 3 5
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_SINGLE_TIDDIT:TIDDIT_SV
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TABIX_BGZIP_TIDDIT_SV
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT
1 1 1
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
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
1 1 1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
1 1 1
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
1 1 1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
80 80
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
1 1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
1 1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSORPRO_MSISOMATIC
1 1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
1 1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
80 80
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2
1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS
1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL
1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL
80 80 80
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
80 80 80
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
1 1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
1 1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
1 1 1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
1 1
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_MUTECT2
1 1
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
1 1 1
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
1 1 1
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
1 1
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
1 1 1
TIDDIT_NORMAL:TIDDIT_SV
1 1
TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV
1 1
TIDDIT_TUMOR:TIDDIT_SV
1 1
TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV
1 1
BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE
1 1
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
12 6 11
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
12 6 11
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
12 6 11
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
12 6 11
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
2 1 2
FASTQ_HLATYPING_OPTITYPE_CUSTOM:YARA_MAPPER_R1
2 2
FASTQ_HLATYPING_OPTITYPE_CUSTOM:YARA_MAPPER_R2
2 2
BAM_MERGE_INDEX_SAMTOOLS_R1:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS_R1:INDEX_MERGE_BAM
2 2
BAM_MERGE_INDEX_SAMTOOLS_R2:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS_R2:INDEX_MERGE_BAM
2 2
FASTQ_HLATYPING_OPTITYPE_CUSTOM:OPTITYPE_CUSTOM
2 2
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE_CUSTOM
2 2
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
2 2 2
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
1 1 1
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
12 6 11
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
12 6 11
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
12 6 11
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
12 6 11
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
12 6 11
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
12 6 11
VCF_ANNOTATE_MERGE:TABIX_TABIX
12 6 11
SAREK:TMB
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:MULTIQC
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
2 2
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE