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	98		98
CRAM_FILTER_LOW_READS:WRITE_PURGE_REPORT	1		1
CRAM_QC_RECAL:SAMTOOLS_STATS	90		90
CRAM_QC_RECAL:MOSDEPTH	90		90
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP	90		90
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM	1		1
AIH_CNV:ClusterPanelRegions	1		1
AIH_CNV:CalcPanelCoverage	45		45
AIH_CNV:ProcessBatch		1		1
AIH_CNV:ModelSingle
AIH_CNV:AggregateBatchData
AIH_CNV:MakeVCFsProbeMerge
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	45		45
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER	225		225
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER	45		45
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	45		45
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	45		45
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE	45		45
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	225		225
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	45		45
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	45		45
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	45		45
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE	225		225
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA	45		45
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME	45		45
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY	180		180
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	180		180
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	180		180
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	180		180
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	180		180
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	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR	45		45
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	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	45		45
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	45		45
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC	45		45
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	225		225
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	45		45
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_tso	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI_catalin	45		45
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED	225		93
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2	45		9
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS	45		9
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL	45		9	1
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL	225		225
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR	225		225
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL	45		45
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR	45		45
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION	45		45
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS	45		9
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	45		45
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ	45		9
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS	45		45
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD	45		45
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2	225		225
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2	45		45
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS	45		45
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL	45		45
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES	225		225
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES	45		45
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION	45		45
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS	45		45
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	45		45
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	45		45
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	45		45
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	45		45
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	45		45
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	45		45
VCF_ANNOTATE_MERGE:TABIX_TABIX	45		45
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY	45		45
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD	45		45
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR	45		45
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS	45		45
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM	45		45
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT	45		45
BAM_CHIP_DETECTION:TABIX_GERMLINE	45		45
BAM_CHIP_DETECTION:TABIX_SOMATIC	45		9
HARMONIZE_GERMLINE:BCFTOOLS_NORM	45		45
HARMONIZE_GERMLINE:BCFTOOLS_SORT	45		45
HARMONIZE_SOMATIC:BCFTOOLS_NORM	45		9
HARMONIZE_SOMATIC:BCFTOOLS_SORT	45		9
HARMONIZE_CHIP_PON:BCFTOOLS_NORM	1		1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT	1		1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE	45		45
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC	45		9
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON	45		8
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS	495		422
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT	495		422
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL	495		422
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY	495		422
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA	45		45
FASTQ_HLATYPING_OPTITYPE:OPTITYPE	45		10
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE	45		9
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP	90		90
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION	45		45
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	495		422
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	495		422
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	495		422
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	495		421
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	495		421
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	495		420
VCF_ANNOTATE_MERGE:TABIX_TABIX	495		419
SAREK:TMB	45		45
SAREK:AGGREGATE_VARIANT_QC	1
SAREK:MULTIQC	1