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gitlab-sarek..un-62017611
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NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_QC_RECAL:SAMTOOLS_STATS
4
CRAM_QC_RECAL:MOSDEPTH
4
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
4
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP
4
1
BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION
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
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DIFF_DV_SENTIEON
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:MERGE_FORCECALLED
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC
2
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
2
1
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
2
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
2
1
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER
2
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION
2
BAM_VARIANT_CALLING_GERMLINE_ALL:GERMLINE_CNV
2
BAM_VARIANT_CALLING_GERMLINE_ALL:BGZIPTABIX_GERMLINE_CNV
2
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_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
2
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
2
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
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
6
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_ALL:MIMSI_ANALYZE
2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2
2
BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER
2
BAM_VARIANT_CALLING_SOMATIC_ALL:EXTRACT_CHROMOSOMES_TNSEQ
2
BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ
2
1
BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS
2
BAM_VARIANT_CALLING_SOMATIC_ALL:FILTER_TNSEQ_VCF_FOR_SOMATIC
2
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_CALLING
2
1
BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF
2
1
BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS
2
1
BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD
2
1
VCF_SOMATIC_SNV_INDEL:PREP_TNSEQ_SNV
2
VCF_SOMATIC_SNV_INDEL:PREP_STRELKA_INDEL
2
VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT
2
VCF_SOMATIC_SNV_INDEL:EXTRACT_CHROMOSOMES
2
VCF_SOMATIC_SNV_INDEL:WHATSHAP
2
VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS
2
VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP
2
VCF_SOMATIC_SNV_INDEL:TABIX_VEP
2
VCF_SOMATIC_SNV_INDEL:LABEL_HOTSPOTS
2
VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO
2
VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF
2
VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL
2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNHAPLOTYPER2
2
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSEQ:SENTIEON_TNFILTER
2
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
2
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
2
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_NORM
2
HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT
2
BAM_CHIP_DETECTION:TABIX_GERMLINE
2
HARMONIZE_GERMLINE:BCFTOOLS_NORM
2
HARMONIZE_GERMLINE: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_CHIP_PON
2
BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES
2
BAM_CHIP_DETECTION:BCFTOOLS_STRIP_FILTER
2
BAM_CHIP_DETECTION:SENTIEON_GENOTYPE
2
BAM_CHIP_DETECTION:TRANSFER_CALLER_AD
2
BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS
2
VCF_DECONFLICT_VARIANTS:DECONFLICT_VARIANTS
2
SAREK:GENERATE_CHIP_REPORT
2
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
14
2
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
14
1
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
14
1
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
14
1
VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE
14
1
VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE
14
2
VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE
14
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
14
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
14
1
VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP
14
3
VCF_ANNOTATE_MERGE:TABIX_TABIX
14
2
VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
2
VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
2
VCF_TMB:TMB
2
SAREK:AGGREGATE_VARIANT_QC
1
SAREK:VARIANT_QC_TO_CSV
1
SAREK:MULTIQC
1
SAREK:WRITE_TRACKER_YML
1