Nextflow Modules
Showing module(s) with keyword "benchmark"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/happy/happy | Process | happy benchmark haplotype validation | Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants. |
| nf-core/happy/prepy | Process | happy benchmark haplotype | Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py |
| nf-core/happy/report | Process | happy benchmark report html variant-calling | Generate standalone HTML benchmarking reports from GA4GH / hap.py variant-calling metrics CSVs |
| nf-core/happy/sompy | Process | happy sompy benchmark haplotype validation somatic variants | Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations. |
| nf-core/modkit/validate | Process | modkit methylation validate nanopore ont modbam ground-truth benchmark | Validate base modification calls in one or more mod-BAMs against a matched ground-truth BED file containing the expected modification state at reference positions. Reports per-sample and combined confusion-matrix style statistics (accuracy, filtered calls, probability distribution) as a tab-separated machine-parseable table. |
| nf-core/truvari/bench | Process | structural variants sv vcf benchmark comparison | Given baseline and comparison sets of variants, calculate the recall/precision/f-measure |
| nf-core/truvari/segment | Process | structural variants sv vcf benchmark normalization | Normalization of SVs into disjointed genomic regions |
| seqera-services/bedtools_intersect | Process | structural variants benchmark bed | Intersect two BED files and require a nonempty result. |
| seqera-services/multiqc | Process | coverage benchmark report | Aggregate supported report files into a MultiQC report. |
| seqera-services/truvari_bench | Process | structural variants benchmark precision and recall | Compare filtered SV calls against an indexed truth VCF. |