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
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
4 4
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
1 1
PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET
1 1 1
PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE
1 1
NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1 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
1 1
SAREK:AGGREGATE_FASTQ_QC
1 1
SAREK:FASTP
1 1
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
32 32
BAM_SENTIEON_DEDUP:SENTIEON_DEDUP
1 1
BAM_POSTDUPLICATES_QC:SEQTOOL_QC
1 1
BAM_QC_PICARD:PICARD_COLLECTMULTIPLEMETRICS
1 1
BAM_QC_PICARD:PICARD_COLLECTHSMETRICS
9 9
BAM_QC_PICARD:PICARD_COLLECTWGSMETRICS
CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
1 1
CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
1 1
SAREK:AGGREGATE_POSTDEDUP_QC
1 1
SAREK:CRAM_TO_BAM
1 1
BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
4 2 2
BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
1 1
BAM_APPLYBQSR:GATK4_APPLYBQSR
3 1 4
CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
1 1
CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
1 1
SAREK:CRAM_TO_BAM_RECAL
1 1
CRAM_QC_RECAL:SAMTOOLS_STATS
1 1
CRAM_QC_RECAL:MOSDEPTH
1 1
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
1 1
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
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_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA
BAM_VARIANT_CALLING_SINGLE_STRELKA:MERGE_STRELKA_GENOME
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TIDDIT_SV
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TABIX_BGZIP_TIDDIT_SV
BAM_VARIANT_CALLING_GERMLINE_ALL:TABIX_VCF_FOR_ENTROPY
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH
1 1
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
3 1 4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2
1
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS
1
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL
1
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES
4 4
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES
1
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION
1
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS
1
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
1 1
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
1
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA:MANTA_TUMORONLY
1 1
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TIDDIT_SV
1 1
BAM_VARIANT_CALLING_SINGLE_TIDDIT:TABIX_BGZIP_TIDDIT_SV
1
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT
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
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_SOMATIC_MANTA:MANTA_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS
BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSORPRO_MSISOMATIC
BAM_VARIANT_CALLING_SOMATIC_ALL:MSISENSOR2_MSI
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION
BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_MUTECT2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
TIDDIT_NORMAL:TIDDIT_SV
TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV
TIDDIT_TUMOR:TIDDIT_SV
TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV
BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
4
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
4
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
4
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
4
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
1 1
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
1 1
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
1 1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
4
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
4
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
4
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
4
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
4
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
4
VCF_ANNOTATE_MERGE:TABIX_TABIX
4
SAREK:TMB
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:MULTIQC
1