Nextflow Modules
Showing module(s) with keyword "machine learning"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/deepsomatic | Process | variant calling machine learning neural network | DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumour and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF file and a tumour somatic gVCF. |
| nf-core/deepvariant/callvariants | Process | variant calling machine learning neural network | Call variants from the examples produced by make_examples |
| nf-core/deepvariant/makeexamples | Process | variant calling machine learning neural network | Transforms the input alignments to a format suitable for the deep neural network variant caller |
| nf-core/deepvariant/postprocessvariants | Process | variant calling machine learning neural network | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data |
| nf-core/deepvariant/rundeepvariant | Process | variant calling machine learning neural network | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data |
| nf-core/deepvariant/vcfstatsreport | Process | variant calling machine learning neural network | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data |
| nf-core/sourcepredict | Process | source tracking metagenomics machine learning | Classifies and predicts the origin of metagenomic samples |
| nf-core/varnet/filter | Process | variant calling machine learning neural network somatic | Finds candidate somatic variants in a tumor/normal pair. This is the first of VarNet's two stages; the candidates it emits are scored by varnet/predict. |
| nf-core/varnet/predict | Process | variant calling machine learning neural network somatic | Scores candidate somatic variants with VarNet's neural network and writes a VCF. This is the second of VarNet's two stages; it consumes the candidates emitted by varnet/filter. |