Processes

PREPARE_GENOME:BWAMEM1_INDEX
PREPARE_GENOME:BWAMEM2_INDEX
PREPARE_GENOME:DRAGMAP_HASHTABLE
PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
PREPARE_GENOME:MSISENSORPRO_SCAN
1
PREPARE_GENOME:MSISENSOR2_SCAN
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
PREPARE_GENOME:UNZIP_LOCI
1
PREPARE_GENOME:UNZIP_GC
1
PREPARE_GENOME:UNZIP_RT
1
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
4
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
2 1
CRAM_QC_RECAL:MOSDEPTH
2 1
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
2 1
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
4
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
1
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
1
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
1
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
1
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
1
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
1
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
4
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
1
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
1
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TIDDIT_SV
1
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TABIX_BGZIP_TIDDIT_SV
1
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
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_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
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
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
1
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
4
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
1
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSORPRO_MSISOMATIC
1
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL
4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
1
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_MUTECT2
1
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
1
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
1
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
1
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
1
TIDDIT_NORMAL:TIDDIT_SV
1
TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV
1
TIDDIT_TUMOR:TIDDIT_SV
1
TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV
1
BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE
1
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
13
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
13
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
13
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
13
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
1 1 1
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
2 1
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
2
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
2 1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
1
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
13
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
13
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
13
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
13
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
13
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
13
VCF_ANNOTATE_MERGE:TABIX_TABIX
13
SAREK:TMB
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:MULTIQC
1