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
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
2
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
SAREK:SPRING_DECOMPRESS_TO_FQ_PAIR
SAREK:SPRING_DECOMPRESS_TO_R1_FQ
SAREK:SPRING_DECOMPRESS_TO_R2_FQ
CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
CONVERT_FASTQ_INPUT:CAT_FASTQ
SAREK:FASTQC
4
SAREK:AGGREGATE_FASTQ_QC
1
SAREK:FASTP
4
FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN
FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM
56
BAM_SENTIEON_DEDUP:SENTIEON_DEDUP
4
BAM_POSTDUPLICATES_QC:SEQTOOL_QC
4
BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS
4
BAM_QC_PICARD:PICARD_COLLECTHSMETRICS
8
BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS
CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
4
CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
4
SAREK:AGGREGATE_POSTDEDUP_QC
1
SAREK:CRAM_TO_BAM
4
BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
8
BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
4
BAM_APPLYBQSR:GATK4_APPLYBQSR
8
CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
4
CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
4
SAREK:CRAM_TO_BAM_RECAL
4
CRAM_QC_RECAL:SAMTOOLS_STATS
4
CRAM_QC_RECAL:MOSDEPTH
4
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
4
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
2
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
2
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
2
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
2
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
4
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
2
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
2
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
4
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
2
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
2
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
8
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
8
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
8
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
8
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
8
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
2
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
4
BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT
2
BAM_VARIANT_CALLING_SOMATIC_FACETS:CONVERT_NORMAL_TO_BAM
2
BAM_VARIANT_CALLING_SOMATIC_FACETS:CONVERT_TUMOR_TO_BAM
2
BAM_VARIANT_CALLING_SOMATIC_FACETS:CNV_FACETS
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT
2
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS
2
BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC
2
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
4
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
2
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
2
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL
4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
4
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
2
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_MUTECT2
2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
2
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
2
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2
4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES
4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
2
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
2
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
2
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
2
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
2
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
2
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
2
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
2
VCF_ANNOTATE_MERGE:TABIX_TABIX
2
VCF_READCOUNT_ANNOTATION:BCFTOOLS_QUERY
2
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_BLOOD
2
VCF_READCOUNT_ANNOTATION:BAMREADCOUNT_TUMOR
2
VCF_READCOUNT_ANNOTATION:ANNOTATE_VCF_READCOUNTS
2
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
2
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
2
BAM_CHIP_DETECTION:TABIX_GERMLINE
2
BAM_CHIP_DETECTION:TABIX_SOMATIC
2
HARMONIZE_GERMLINE:BCFTOOLS_NORM
2
HARMONIZE_GERMLINE:BCFTOOLS_SORT
2
HARMONIZE_SOMATIC:BCFTOOLS_NORM
2
HARMONIZE_SOMATIC:BCFTOOLS_SORT
2
HARMONIZE_CHIP_PON:BCFTOOLS_NORM
1
HARMONIZE_CHIP_PON:BCFTOOLS_SORT
1
VCF_MERGE_CHARACTERISTICS:MERGE_GERMLINE
2
VCF_MERGE_CHARACTERISTICS:MERGE_SOMATIC
2
VCF_MERGE_CHARACTERISTICS:MERGE_CHIP_PON
2
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
22
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
22
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
22
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
22
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
4
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
2
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
22
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
22
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
22
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
22
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
22
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
22
VCF_ANNOTATE_MERGE:TABIX_TABIX
22
SAREK:TMB
2
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:MULTIQC
1