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	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
CRAM_QC_RECAL:SAMTOOLS_STATS	94	47
CRAM_QC_RECAL:MOSDEPTH	94	94
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP	94	94
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM	1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	48	47
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	48	47
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	48	5
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	48	47
BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER	240	47
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER	48
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	48
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	48
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE	48	47
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER	240	236
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS	48
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS	48
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES	48
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE	240	237
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA	48	43
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME	48	43
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY	192	47
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY	192
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP	192
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION	192
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX	192
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	46	46
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT	46	7
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	46
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH	46		3
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL	46
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT	46
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS	46
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC	46
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC	230
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS	46
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS	46
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED	230
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL	230	215
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR	230	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL	46	13
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION	46
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS	46
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_MUTECT2	46
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2	46
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER	46
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING	46
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD	46
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2	240	47
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2	48
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS	48
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL	48
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES	240	236
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES	48	29
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION	48
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS	48
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	48
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	48
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	48
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	48
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	48
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	48
VCF_ANNOTATE_MERGE:TABIX_TABIX	48
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY	48
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD	48
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR	46
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS	46
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM	46
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT	46
BAM_CHIP_DETECTION:TABIX_GERMLINE	46
BAM_CHIP_DETECTION:TABIX_SOMATIC	46
HARMONIZE_GERMLINE:BCFTOOLS_NORM	46
HARMONIZE_GERMLINE:BCFTOOLS_SORT	46
HARMONIZE_SOMATIC:BCFTOOLS_NORM	46
HARMONIZE_SOMATIC:BCFTOOLS_SORT	46
HARMONIZE_CHIP_PON:BCFTOOLS_NORM	1	1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT	1	1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE	46
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC	46
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON	46
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS	514
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT	514
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL	514
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY	514
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP	94	94
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION	46
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE	514
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE	514
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE	514
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF	514
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX	514
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP	514
VCF_ANNOTATE_MERGE:TABIX_TABIX	514
SAREK:TMB	46
SAREK:AGGREGATE_VARIANT_QC	1
SAREK:MULTIQC	1