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		1
PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT	5		5
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED	1		1
PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET	1		1
PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE	1		1
NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET	1		1
CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT	90		90
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT	1		1
CRAM_QC_RECAL:SAMTOOLS_STATS	78		78
CRAM_QC_RECAL:MOSDEPTH	78		78
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP	78		78
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM	1		1
AIH_CNV:ClusterPanelRegions	1		1
AIH_CNV:CalcPanelCoverage	39		39
AIH_CNV:ProcessBatch		1		1
AIH_CNV:ModelSingle
AIH_CNV:AggregateBatchData
AIH_CNV:MakeVCFsProbeMerge
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	39		39
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER	195		195
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER	39		39
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	39		39
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	39		39
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE	39		39
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	195		195
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	39		39
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	39		39
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	39		39
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE	195		195
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA	39		39
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME	39		39
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY	156		156
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	156		156
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	156		156
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	156		156
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	156		156
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	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR	39		39
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	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	39		39
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	39		39
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC	39		39
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	195		195
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	39		39
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin	39		39
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED	195		41
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2	39
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS	39
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL	39			1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL	195		195
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR	195		195
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL	39		39
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR	39		39
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION	39		39
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS	39
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	39		39
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ	39
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS	39		39
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD	39		39
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2	195		195
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2	38		38
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS	39		39
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL	39		39
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES	195		195
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES	39		39
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION	39		39
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS	39		39
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	39		39
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	39		39
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	39		39
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	39		39
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	39		39
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	39		39
VCF_ANNOTATE_MERGE:TABIX_TABIX	38		38
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY	39		39
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD	39		39
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR	39		38	1
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS	39		38
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM	39		38
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT	39		38
BAM_CHIP_DETECTION:TABIX_GERMLINE	39		39
BAM_CHIP_DETECTION:TABIX_SOMATIC	39
HARMONIZE_GERMLINE:BCFTOOLS_NORM	39		39
HARMONIZE_GERMLINE:BCFTOOLS_SORT	39		39
HARMONIZE_SOMATIC:BCFTOOLS_NORM	39
HARMONIZE_SOMATIC:BCFTOOLS_SORT	39
HARMONIZE_CHIP_PON:BCFTOOLS_NORM	1		1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT	1		1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE	39		38
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC	39
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON	39
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS	429		351
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT	429		351
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL	429		351
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY	429		351
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA	39		39
FASTQ_HLATYPING_OPTITYPE:OPTITYPE	39		3
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE	39		3
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP	78		78
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION	39		39
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	429		351
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	429		351
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	429		351
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	429		351
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	429		351
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	429		351
VCF_ANNOTATE_MERGE:TABIX_TABIX	429		351
SAREK:TMB	39		39
SAREK:AGGREGATE_VARIANT_QC	1
SAREK:MULTIQC	1