Processes


PREPARE_GENOME:BWAMEM1_INDEX
PREPARE_GENOME:BWAMEM2_INDEX
PREPARE_GENOME:DRAGMAP_HASHTABLE
PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
PREPARE_GENOME:MSISENSORPRO_SCAN
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
PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT	69		69
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_QC_RECAL:SAMTOOLS_STATS	8		8	2
CRAM_QC_RECAL:MOSDEPTH	8		8
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP	8		6	2
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM	1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	4		4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	4		4	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	4		4	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	4		4	4
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER	276		276
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER	4		4	2
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	4		4	4
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	4		4	4
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE	4		4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	276		276
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	4		4	3
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	4		4	4
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	4		4	4
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY	16		15	16
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	16		15	16
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	16		7	16
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	16			12
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	16			12
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:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT	4		4
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	4			4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	4		4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	4		4	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	4		4	4
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	4		4	4
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC	4		4
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI	4			4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED	276		276
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2	4		4	4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS	4		4	4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL	4		4	4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL	276		276
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR	276		276
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL	4		4	2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR	4		4	4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION	4		4	4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS	4		4	4
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_MUTECT2	4		2	4
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	4		4
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	4		4	4
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING	4			4
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD	4			4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2	276		276
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2	4		4	4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS	4		4	4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL	4		4	4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES	276		276
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES	4		4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION	4		4	2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS	4		4	4
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	4		4	3
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	4		4	4
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	4		4	4
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	4		4	4
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	4		4	4
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	4		4	4
VCF_ANNOTATE_MERGE:TABIX_TABIX	4		4	4
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY	4		4	4
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD	4		4	4
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR	4		4	4
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS	4			4
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM	4			4
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT	4			4
BAM_CHIP_DETECTION:TABIX_GERMLINE	4			4
BAM_CHIP_DETECTION:TABIX_SOMATIC	4		4	4
HARMONIZE_GERMLINE:BCFTOOLS_NORM	4			4
HARMONIZE_GERMLINE:BCFTOOLS_SORT	4			4
HARMONIZE_SOMATIC:BCFTOOLS_NORM	4		4	4
HARMONIZE_SOMATIC:BCFTOOLS_SORT	4		4	4
HARMONIZE_CHIP_PON:BCFTOOLS_NORM	1		1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT	1		1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE	4			4
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC	4			4
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON	4			4
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS	44		24	34
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT	44		24	34
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL	44		24	34
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY	44		24	34
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA	4		4
FASTQ_HLATYPING_OPTITYPE:OPTITYPE	3	1	2	4
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE	3			2
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP	8		8	2
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION	4		4	4
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	44		24	34
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	44		24	34
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	44		24	34
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	44		20	34
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	44		20	32
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	44		20	33
VCF_ANNOTATE_MERGE:TABIX_TABIX	44		20	32
SAREK:TMB
SAREK:AGGREGATE_VARIANT_QC	1			1
SAREK:MULTIQC
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE	276		275	113
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA	4		3	4
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME	4		3	4
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	276		275	235
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	4		3	4
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	4		3	4