Processes

PREPARE_GENOME:BWAMEM1_INDEX
PREPARE_GENOME:BWAMEM2_INDEX
PREPARE_GENOME:DRAGMAP_HASHTABLE
PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
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
PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
5
PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
1
NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET
1
CRAM_QC_RECAL:SAMTOOLS_STATS
240 35
CRAM_QC_RECAL:MOSDEPTH
240 18
BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER
1200 109
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS
240
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_GVCFS
VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY
240
VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP
240 13
VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION
240
VCF_ANNOTATE_INDEL_ENTROPY:TABIX_TABIX
240
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER
240
BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_ESTIMATE_SEX
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL
BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_TUMOR
BAM_VARIANT_CALLING_SOMATIC_ALL:SAMTOOLS_CONVERT_CRAM_TO_BAM
VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
240
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
240
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
240
VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
240
CRAM_HLATYPING_ALL:CRAM_FILTER_HLA
240 16
FASTQ_HLATYPING_OPTITYPE:OPTITYPE
240
CRAM_HLATYPING_ALL:HLA_CONVERT_OPTITYPE
240
SAREK:MULTIQC
1