Description of feature

local:

• add_info_to_vcf
• build_intervals
• create_intervals_bed

nf-core:

• ascat
• bcftools/annotate
• bcftools/concat
• bcftools/mpileup
• bcftools/sort
• bcftools/stats
• bwa/index
• bwa/mem
• bwamem2/index
• bwamem2/mem
• cat/cat
• cat/fastq
• cnvkit/antitarget
• cnvkit/batch
• cnvkit/genemetrics
• cnvkit/reference
• controlfreec/assesssignificance
• controlfreec/freec
• controlfreec/freec2bed
• controlfreec/freec2circos
• controlfreec/makegraph
• custom/dumpsoftwareversions
• deepvariant
• dragmap/align
• dragmap/hashtable
• ensemblvep/download
• ensemblvep/vep
• fastp
• fastqc
• fgbio/callmolecularconsensusreads
• fgbio/fastqtobam
• fgbio/groupreadsbyumi
• freebayes
• gatk4/applybqsr
• gatk4/applyvqsr
• gatk4/baserecalibrator
• gatk4/calculatecontamination
• gatk4/cnnscorevariants
• gatk4/createsequencedictionary
• gatk4/estimatelibrarycomplexity
• gatk4/filtermutectcalls
• gatk4/filtervarianttranches
• gatk4/gatherbqsrreports
• gatk4/gatherpileupsummaries
• gatk4/genomicsdbimport
• gatk4/genotypegvcfs
• gatk4/getpileupsummaries
• gatk4/haplotypecaller
• gatk4/intervallisttobed
• gatk4/learnreadorientationmodel
• gatk4/markduplicates
• gatk4/mergemutectstats
• gatk4/mergevcfs
• gatk4/mutect2
• gatk4/variantrecalibrator
• gatk4spark/applybqsr
• gatk4spark/baserecalibrator
• gatk4spark/markduplicates
• manta/germline
• manta/somatic
• manta/tumoronly
• mosdepth
• msisensorpro/msisomatic
• msisensorpro/scan
• multiqc
• ngscheckmate/ncm
• samblaster
• samtools/bam2fq
• samtools/collatefastq
• samtools/convert
• samtools/faidx
• samtools/index
• samtools/merge
• samtools/mpileup
• samtools/stats
• samtools/view
• sentieon/applyvarcal
• sentieon/bwamem
• sentieon/dedup
• sentieon/dnamodelapply
• sentieon/dnascope
• sentieon/gvcftyper
• sentieon/haplotyper
• sentieon/varcal
• snpeff/download
• snpeff/snpeff
• strelka/germline
• strelka/somatic
• svdb/merge
• tabix/bgziptabix
• tabix/tabix
• tiddit/sv
• untar
• unzip
• vcftools