DarwinOmics.ai

Workflow-scale analysis elements

Pipelines & Workflow Elements

nf-core/imported pipelines, Darwinomics executable pipeline contracts, Darwin catalog workflow wrappers, BioNeMo workflows, prototypes, and workflow engine support. The full count is workflow-scale elements; named imported pipelines are shown where the source is a complete workflow.

nf-coreRNA-seqSingle-cellWGSATAC-seqBioNeMo
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Align Bwa Mem Just BWA-MEM alignment, no variant calling. Pipelines & Workflow Elements Runnable sequencing reads lh3/bwa | 1,753 stars Align Bwa Mem2 Align Bwa Mem2 handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable sequencing reads lh3/bwa | 1,753 stars Align Hisat2 Just HISAT2 alignment (low memory). Pipelines & Workflow Elements Runnable sequencing reads DaehwanKimLab/hisat2 | 539 stars Align Minimap2 Just minimap2 alignment for long reads. Pipelines & Workflow Elements Runnable sequencing reads Align Star Just STAR alignment for RNA-seq. Pipelines & Workflow Elements Runnable sequencing reads alexdobin/STAR | 2,216 stars Alignment Only Just alignment without downstream analysis. Use when you only need BAM files. Pipelines & Workflow Elements Runnable sequencing reads AlphaFold2 Protein structure prediction using AlphaFold2. Pipelines & Workflow Elements Runnable protein or structure data google-deepmind/alphafold | 14,697 stars AlphaFold3 Protein complex structure prediction using AlphaFold3. Pipelines & Workflow Elements Runnable protein or structure data google-deepmind/alphafold3 | 8,276 stars Annotate Variants Annotate Variants handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads ATAC-seq ATAC-seq analysis: QC -> trimming -> alignment -> duplicate removal -> peak calling. Identifies open chromatin regions. Pipelines & Workflow Elements Runnable aligned sequencing reads ATAC-seq Bwa Mem2 ATAC-seq Bwa Mem2 handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable sequencing reads lh3/bwa | 1,753 stars Cell Line Specific Splicing Design pipeline cell line specific splicing design Pipelines & Workflow Elements Runnable Workflow Cell Segmentation Segment cells from microscopy images using Cellpose deep learning model. Pipelines & Workflow Elements Runnable image or spatial data Cellpose Cellpose processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable image or spatial data ChIP-seq ChIP-seq analysis: QC -> trimming -> alignment -> peak calling -> annotation. Identifies protein-DNA binding sites. Pipelines & Workflow Elements Runnable aligned sequencing reads ChIP-seq Broad ChIP-seq with broad peak calling for histone modifications (H3K27me3, H3K9me3). Pipelines & Workflow Elements Runnable aligned sequencing reads ChIP-seq Bwa Mem2 ChIP-seq using BWA-MEM2 for alignment. Pipelines & Workflow Elements Runnable sequencing reads lh3/bwa | 1,753 stars ChIP-seq Control Free ChIP-seq peak calling without control sample. Pipelines & Workflow Elements Runnable aligned sequencing reads ChIP-seq Narrow ChIP-seq narrow peak calling for transcription factors. Pipelines & Workflow Elements Runnable aligned sequencing reads Colabfold Protein structure prediction using ColabFold. Pipelines & Workflow Elements Runnable Workflow Complexa Binder Design Complexa Binder Design applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Complexa Sweep Complexa Sweep coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Cutandrun CUT&RUN epigenomics pipeline for mapping protein-DNA interactions with lower background than ChIP-seq. Pipelines & Workflow Elements Runnable Workflow Cutandtag CUT&Tag epigenomics pipeline for mapping histone modifications and transcription factors. Pipelines & Workflow Elements Runnable Workflow Darwin Abotyper ABO and Rh blood group typing from whole-genome or targeted sequencing data. Pipelines & Workflow Elements Runnable Workflow Darwin Alevin Fry Accurate and memory-efficient single-cell RNA-seq quantification using Alevin-Fry with selective alignment Pipelines & Workflow Elements Runnable Workflow COMBINE-lab/salmon | 901 stars Darwin Alleleexpression Allele-specific gene expression analysis from RNA-seq data using phased variants and read-backed phasing. Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin AlphaFold2 Protein structure prediction from amino acid sequence using evolutionary information and deep learning. Pipelines & Workflow Elements Runnable protein or structure data google-deepmind/alphafold | 14,697 stars Darwin AlphaFold3 Unified structure prediction for proteins, DNA, RNA, and small molecules using diffusion-based architecture. Pipelines & Workflow Elements Runnable protein or structure data google-deepmind/alphafold3 | 8,276 stars Darwin Alphamissense Deep learning model classifying missense variants as likely pathogenic or benign using AlphaFold2. Pipelines & Workflow Elements Runnable Workflow google-deepmind/alphafold | 14,697 stars Darwin Alphaproteo AI system for designing novel protein binders with high affinity to specified target proteins. Pipelines & Workflow Elements Runnable Workflow Darwin Archr Tool Single-cell ATAC-seq analysis with ArchR: fragment-level processing, peak calling, dimensionality reduction, gene scoring, and trajectory inference Pipelines & Workflow Elements Runnable Workflow Darwin Bacass Complete bacterial genome assembly from short reads with QC, assembly via Unicycler, annotation with Prokka, and quality reporting. Pipelines & Workflow Elements Runnable Workflow Darwin Bactmap Mapping of bacterial short reads to a reference genome for SNP calling, phylogenetics, and outbreak analysis. Pipelines & Workflow Elements Runnable Workflow Darwin Bamtofastq Convert BAM/CRAM files back to FASTQ format with optional read sorting and QC. Pipelines & Workflow Elements Runnable Workflow Darwin BioNeMo Boltz2 NVIDIA NIM-hosted Boltz-2 for next-generation biomolecular structure prediction. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Deepvariant NVIDIA NIM-hosted Google DeepVariant for accurate germline variant calling from short reads. Pipelines & Workflow Elements Runnable aligned sequencing reads google/deepvariant | 3,740 stars Darwin BioNeMo Diffdock NVIDIA NIM-hosted DiffDock diffusion-based molecular docking for drug discovery. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Evo2 NVIDIA NIM-hosted Evo2 genomic foundation model for sequence generation and variant scoring. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Genmol NVIDIA NIM-hosted GenMol for fragment-based and de novo molecule generation for drug discovery. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Molmim NVIDIA NIM-hosted MolMIM for controlled small molecule generation using mutual information machine. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Openfold3 NVIDIA NIM-hosted OpenFold3 for biomolecular complex structure prediction. Pipelines & Workflow Elements Runnable Workflow aqlaboratory/openfold | 3,391 stars Darwin BioNeMo Proteina Complexa NVIDIA NIM-hosted Proteina Complexa for multi-chain protein complex structure and interaction prediction. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Proteinmpnn NVIDIA NIM-hosted ProteinMPNN for inverse folding and sequence design from protein backbones. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin BioNeMo Rnapro NVIDIA NIM-hosted RNA-protein interaction prediction model for regulatory element analysis. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwin Boltz Boltz unified architecture for protein and nucleic acid structure prediction with confidence estimation. Pipelines & Workflow Elements Runnable Workflow Darwin Boltz1 Open-source model predicting structures of proteins, nucleic acids, and small molecules with confidence. Pipelines & Workflow Elements Runnable Workflow Darwin Boltz2 Next-generation biomolecular structure prediction with improved accuracy for multi-chain complexes. Pipelines & Workflow Elements Runnable Workflow Darwin Boltzgen Generative model combining Boltz architecture with conditional generation for protein structure design. Pipelines & Workflow Elements Runnable Workflow Darwin Borzoi Deep learning model predicting cell-type specific gene expression from 524kb genomic sequences. Pipelines & Workflow Elements Runnable Workflow Darwin Caduceus Bidirectional equivariant long-range DNA sequence model based on Mamba state-space architecture. Pipelines & Workflow Elements Runnable Workflow Darwin Cageseq CAGE-seq analysis for genome-wide transcription start site mapping and promoter activity quantification. Pipelines & Workflow Elements Runnable Workflow Darwin Callingcards Calling Cards assay analysis for mapping transcription factor binding sites using transposon-based insertional profiling. Pipelines & Workflow Elements Runnable Workflow Darwin Cell2location Bayesian model for mapping cell types to spatial transcriptomics data using scRNA-seq reference. Pipelines & Workflow Elements Runnable Workflow Darwin Cellpainting High-content cell painting image analysis for morphological profiling, feature extraction, and compound activity assessment. Pipelines & Workflow Elements Runnable Workflow Darwin Cellplm Pre-trained language model encoding single cells as sequence tokens for transcriptomic analysis. Pipelines & Workflow Elements Runnable Workflow Darwin Cellrank Tool Fate mapping and trajectory analysis with CellRank: RNA velocity-guided fate probability estimation and terminal state identification Pipelines & Workflow Elements Runnable Workflow Darwin Chai1 Foundation model for molecular structure prediction supporting proteins, nucleic acids, and cofactors. Pipelines & Workflow Elements Runnable Workflow Darwin Chroma Programmable diffusion model for protein design conditioned on structure, sequence, and function. Pipelines & Workflow Elements Runnable Workflow Darwin Chromap Tool Ultra-fast alignment and preprocessing of chromatin accessibility data with Chromap: ATAC-seq, CUT&RUN, and Hi-C alignment with barcode processing Pipelines & Workflow Elements Runnable Workflow Darwin Circrna Genome-wide detection, quantification, and functional annotation of circular RNAs from RNA-seq data. Pipelines & Workflow Elements Runnable Workflow Darwin Clipseq Analysis of CLIP-seq and eCLIP data for mapping RNA-protein interactions and identifying binding sites of RNA-binding proteins. Pipelines & Workflow Elements Runnable Workflow Darwin Colabfold Fast protein structure prediction using MMseqs2-based MSA generation and AlphaFold2 or RoseTTAFold. Pipelines & Workflow Elements Runnable Workflow Darwin Comet Tool Open-source tandem mass spectrometry database search with Comet: sequence database searching for peptide identification Pipelines & Workflow Elements Runnable Workflow Darwin Coproid Identification of organisms from ancient coprolite DNA using metagenomic profiling and source tracking. Pipelines & Workflow Elements Runnable Workflow Darwin Createpanelrefs Build panel of normals reference files for somatic variant calling from a cohort of normal samples. Pipelines & Workflow Elements Runnable Workflow Darwin Createtaxdb Build custom taxonomic databases for Kraken2, DIAMOND, or MALT from NCBI or custom genome collections. Pipelines & Workflow Elements Runnable Workflow Darwin Datasync Automated download and synchronisation of genomic datasets from SRA, ENA, or NCBI with integrity verification. Pipelines & Workflow Elements Runnable Workflow Darwin Deepmicro Deep representation learning for microbiome data supporting disease prediction and feature selection. Pipelines & Workflow Elements Runnable Workflow Darwin Deepmodeloptim Hyperparameter optimisation and neural architecture search for genomics deep learning models using Optuna. Pipelines & Workflow Elements Runnable Workflow Darwin Deepmutscan Analysis of deep mutational scanning experiments to characterise the fitness landscape of protein variants. Pipelines & Workflow Elements Runnable Workflow Darwin Denovotranscript De novo assembly of transcriptomes from RNA-seq reads using Trinity with QC, completeness assessment, and expression quantification. Pipelines & Workflow Elements Runnable Workflow Darwin DESeq2 Research-certified Darwin catalog wrapper over darwinomics-tool-deseq2. It emits exact DESeq2 1.52.0 default Wald fixture parity rows for the active certified count matrix and fails closed outside that certificate. Pipelines & Workflow Elements Runnable expression matrices thelovelab/DESeq2 | 465 stars Darwin Detaxizer Taxonomic decontamination of metagenomic samples by identifying and removing reads from unwanted organisms. Pipelines & Workflow Elements Runnable Workflow Darwin Dialignr Tool Reference-free chromatogram alignment for DIA proteomics with DIAlignR: dynamic time warping alignment of extracted ion chromatograms Pipelines & Workflow Elements Runnable sequencing reads Darwin Diaproteomics Data-independent acquisition (DIA) proteomics analysis using spectral library generation, OpenSWATH, and PyProphet for quantitative proteomics. Pipelines & Workflow Elements Runnable Workflow Darwin Diseasemodulediscovery Network-based disease module discovery from multi-omics expression data using co-expression and PPI networks Pipelines & Workflow Elements Runnable Workflow Darwin Dnabert2 Efficient pre-trained DNA language model with multi-species genome data using BPE tokenization. Pipelines & Workflow Elements Runnable Workflow jerryji1993/DNABERT | 761 stars Darwin Drop Multi-omics RNA outlier detection covering aberrant expression, aberrant splicing, and mono-allelic expression Pipelines & Workflow Elements Runnable Workflow Darwin Drugresponseeval Benchmark and evaluate drug response prediction models using cell line viability data Pipelines & Workflow Elements Runnable Workflow Darwin Easypqp Tool Spectral library generation for DIA proteomics with EasyPQP: retention time alignment, library calibration, and OpenSWATH-compatible output Pipelines & Workflow Elements Runnable Workflow Darwin Edger Tool Research-certified Darwin catalog wrapper over darwinomics-tool-edger. It emits exact edgeR 4.10.1 GLM quasi-likelihood topTags fixture parity rows for the active certified count matrix and fails closed outside that certificate. Pipelines & Workflow Elements Runnable expression matrices Darwin Enformer Deep learning model predicting gene expression and chromatin accessibility from 200kb DNA sequences. Pipelines & Workflow Elements Runnable Workflow Darwin Esm Cambrian Next-generation ESM model with improved long-context understanding and structural reasoning. Pipelines & Workflow Elements Runnable Workflow facebookresearch/esm | 4,140 stars Darwin Esm1v Protein language model for zero-shot prediction of variant effects from sequence alone. Pipelines & Workflow Elements Runnable Workflow Darwin Esm2 Evolutionary Scale Model 2: state-of-the-art protein language model with up to 15B parameters. Pipelines & Workflow Elements Runnable Workflow facebookresearch/esm | 4,140 stars Darwin Esm3 Multimodal foundation model for proteins jointly reasoning over sequence, structure, and function. Pipelines & Workflow Elements Runnable Workflow Darwin Esmfold Single-sequence protein structure prediction using the ESM-2 language model — no MSA required. Pipelines & Workflow Elements Runnable protein or structure data facebookresearch/esm | 4,140 stars Darwin Eve Model Unsupervised deep generative model estimating variant pathogenicity from evolutionary data. Pipelines & Workflow Elements Runnable Workflow Darwin Evexplorer Characterisation and analysis of extracellular vesicles from multi-modal profiling data Pipelines & Workflow Elements Runnable Workflow Darwin Evo2 7B parameter genomic foundation model trained on 9.3T nucleotide tokens across the tree of life. Pipelines & Workflow Elements Runnable Workflow Darwin Evodiff Discrete diffusion model for evolutionary-guided protein sequence generation and design. Pipelines & Workflow Elements Runnable Workflow Darwin Fastqrepair Repair corrupted or truncated FASTQ files and recover usable reads Pipelines & Workflow Elements Runnable Workflow Darwin Fastquorum Consensus sequence generation from duplex and molecular-barcoded sequencing reads for error-corrected variant calling Pipelines & Workflow Elements Runnable Workflow Darwin Geneformer Context-aware attention-based model pre-trained on 29.9M human single-cell transcriptomes. Pipelines & Workflow Elements Runnable Workflow Darwin Generator Genomic Autoregressive genomic sequence generator for synthesizing realistic DNA sequences. Pipelines & Workflow Elements Runnable Workflow Darwin Genie2 Hierarchical diffusion model for protein backbone generation with shape and topology control. Pipelines & Workflow Elements Runnable Workflow Darwin Genomeassembler De novo genome assembly pipeline supporting HiFi, ONT, and hybrid sequencing with QC and scaffolding Pipelines & Workflow Elements Runnable sequencing reads Darwin Genomeqc Comprehensive genome sequencing quality control with coverage, insert size, and duplication metrics Pipelines & Workflow Elements Runnable Workflow Darwin Genomeskim Low-coverage genome skimming for organellar genome assembly, ploidy estimation, and repeat content Pipelines & Workflow Elements Runnable Workflow Darwin Genomicrelatedness Estimate kinship, IBD sharing, and population structure from SNP array or WGS data Pipelines & Workflow Elements Runnable Workflow Darwin Giotto Tool Spatial multi-omics analysis with Giotto: spatial clustering, cell-type deconvolution, spatial gene expression patterns, and niche analysis Pipelines & Workflow Elements Runnable Workflow Darwin Gnina CNN-based molecular docking with deep learning scoring for structure-based drug discovery. Pipelines & Workflow Elements Runnable Workflow Darwin Grover Graph neural network for learning molecular representations of genomic regulatory elements. Pipelines & Workflow Elements Runnable Workflow Darwin Hadge Unified demultiplexing pipeline combining hashtag oligo and genotype-based methods for pooled single-cell experiments Pipelines & Workflow Elements Runnable Workflow Darwin Hgtseq Detection and characterisation of horizontal gene transfer events from metagenomic and host sequencing data Pipelines & Workflow Elements Runnable Workflow Darwin Hyenadna Long-range genomic language model using hyena operators, scaling to 1M token context. Pipelines & Workflow Elements Runnable Workflow Darwin Imcyto Full analysis pipeline for Imaging Mass Cytometry data: segmentation, cell phenotyping, and spatial analysis Pipelines & Workflow Elements Runnable Workflow Darwin Kallisto Bustools Ultra-fast single-cell RNA-seq quantification using kallisto bus and bustools for barcode/UMI processing Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Kmermaid k-mer sketching and comparison of genomic sequences using sourmash for fast similarity search and containment analysis. Pipelines & Workflow Elements Runnable Workflow Darwin Limma Tool Research-certified Darwin catalog wrapper over darwinomics-tool-limma. It emits exact limma 3.68.4 plus edgeR 4.10.1 voom fixture parity rows for the active certified count matrix and fails closed outside that certificate. Pipelines & Workflow Elements Runnable expression matrices Darwin Longraredisease Rare disease variant calling from long-read sequencing including SNVs, SVs, repeat expansions, and methylation Pipelines & Workflow Elements Runnable Workflow Darwin Lsmquant Automated image analysis and cell quantification from light-sheet fluorescence microscopy data Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Macs3 Tool ChIP-seq, ATAC-seq, and CUT&RUN peak calling with MACS3: improved statistical model for calling narrow and broad peaks Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Magmap Read mapping, abundance quantification, and taxonomic annotation of metagenome-assembled genomes Pipelines & Workflow Elements Runnable Workflow Darwin Marsseq Processing pipeline for MARS-seq massively parallel single-cell RNA-seq data Pipelines & Workflow Elements Runnable Workflow Darwin Mcmicro End-to-end multiplexed tissue imaging pipeline: illumination correction, stitching, segmentation, and cell quantification Pipelines & Workflow Elements Runnable Workflow Darwin Meerpipe Automated pulsar timing analysis pipeline for MeerKAT radio telescope data Pipelines & Workflow Elements Runnable Workflow Darwin Metaboigniter End-to-end LC-MS metabolomics pipeline with feature detection, alignment, identification, and statistical analysis Pipelines & Workflow Elements Runnable Workflow Darwin Metapep Metaproteomics pipeline for peptide identification, quantification, and functional annotation from environmental samples Pipelines & Workflow Elements Runnable Workflow Darwin Metatdenovo De novo assembly and annotation of metatranscriptomes from environmental RNA-seq data Pipelines & Workflow Elements Runnable Workflow Darwin Methylarray End-to-end analysis of Illumina methylation array data: IDAT import, normalization, differential methylation, and reporting. Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Methylong Comprehensive CpG and non-CpG methylation calling from Oxford Nanopore and PacBio HiFi long-read data Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Mhcquant Quantitative identification of MHC-presented peptides from LC-MS/MS data using Comet, Percolator, and MHCflurry for neoantigen discovery. Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Mitodetect Detection and annotation of mitochondrial DNA variants including heteroplasmy from WGS or mtDNA-enriched sequencing Pipelines & Workflow Elements Runnable Workflow Darwin Mnaseseq Micrococcal nuclease sequencing for genome-wide nucleosome positioning, occupancy, and phasing analysis Pipelines & Workflow Elements Runnable Workflow Darwin Molkart Single-molecule spatial transcriptomics analysis pipeline for multiplexed tissue imaging, spot calling, and cell segmentation. Pipelines & Workflow Elements Runnable Workflow Darwin Monocle3 Single-cell trajectory analysis with Monocle3: pseudotime ordering, branch point detection, and differential expression along trajectories Pipelines & Workflow Elements Runnable Workflow Darwin Mothur Tool OTU-based microbial community analysis with mothur: sequence alignment, chimera removal, OTU clustering, and diversity statistics Pipelines & Workflow Elements Runnable Workflow Darwin Mrnet Multi-resolution network for integrating spatial and single-cell transcriptomics. Pipelines & Workflow Elements Runnable Workflow Darwin Msconvert Tool ProteoWizard MSConvert: vendor-format mass spectrometry file conversion with peak picking, centroiding, and filtering to mzML/mzXML/MGF Pipelines & Workflow Elements Runnable Workflow Darwin Msstats Tool Statistical analysis of quantitative proteomics data with MSstats: protein-level differential abundance testing with sample-level modeling Pipelines & Workflow Elements Runnable Workflow Darwin Multiplesequencealign Benchmark and produce multiple sequence alignments using a range of tools with downstream phylogenetic inference Pipelines & Workflow Elements Runnable sequencing reads Darwin Multivi Variational autoencoder for joint analysis of RNA, ATAC, and protein in single cells. Pipelines & Workflow Elements Runnable Workflow Darwin Nanostring Analysis of NanoString nCounter gene expression data including QC, normalization, and differential expression. Pipelines & Workflow Elements Runnable Workflow Darwin Nascent Genome-wide analysis of nascent RNA transcription using GRO-seq or PRO-seq for studying active transcription and RNA Pol II dynamics. Pipelines & Workflow Elements Runnable Workflow Darwin Nicheformer Foundation model integrating single-cell and spatial transcriptomics for niche-aware cell analysis. Pipelines & Workflow Elements Runnable Workflow Darwin Nucleotide Transformer Foundation model for genomics trained on 2.5B nucleotides across human and multispecies genomes. Pipelines & Workflow Elements Runnable Workflow Darwin Nucleotide Transformer V2 Updated Nucleotide Transformer with improved fine-tuning efficiency and downstream task performance. Pipelines & Workflow Elements Runnable Workflow Darwin Omegafold High-resolution de novo protein structure prediction from single sequence using pre-trained PLM weights. Pipelines & Workflow Elements Runnable Workflow Darwin Omicsgenetraitassociation Multi-omics integration pipeline for gene-trait association testing including eQTL, pQTL, and mQTL analyses Pipelines & Workflow Elements Runnable Workflow Darwin Omnicell Foundation model for multi-modal single-cell data integration and cross-modality prediction. Pipelines & Workflow Elements Runnable Workflow Darwin Oncoanalyser Comprehensive somatic cancer genome analysis: purity/ploidy, copy number, structural variants, signatures, and tissue of origin Pipelines & Workflow Elements Runnable Workflow Darwin Openfold Open-source reimplementation of AlphaFold2 with support for fine-tuning and custom training. Pipelines & Workflow Elements Runnable Workflow aqlaboratory/openfold | 3,391 stars Darwin Openmm High-performance molecular dynamics simulation toolkit for biomolecular systems. Pipelines & Workflow Elements Runnable Workflow Darwin Openms Tool Comprehensive proteomics data analysis framework with OpenMS: LC-MS feature detection, alignment, quantification, and identification Pipelines & Workflow Elements Runnable Workflow Darwin Openswath Tool Data-independent acquisition proteomics analysis with OpenSWATH: targeted extraction, scoring, and quantification from SWATH/DIA data Pipelines & Workflow Elements Runnable Workflow Darwin Pacvar Comprehensive variant calling from PacBio HiFi long reads: SNVs, indels, SVs, repeat expansions, and phasing Pipelines & Workflow Elements Runnable Workflow Darwin Pairgenomealign Pairwise whole-genome alignment using LAST or minimap2 for comparative genomics and synteny analysis. Pipelines & Workflow Elements Runnable sequencing reads Darwin Pangenome Build and analyse pangenome variation graphs from multiple genome assemblies using PGGB and odgi. Pipelines & Workflow Elements Runnable Workflow Darwin Panoramaseq Integration and analysis of multi-modal single-cell data including RNA, ATAC, and protein measurements Pipelines & Workflow Elements Runnable Workflow Darwin Pathogensurveillance Whole-genome sequencing-based pathogen surveillance: assembly, typing, AMR detection, and phylogenetics Pipelines & Workflow Elements Runnable Workflow Darwin Percolator Tool Machine learning-based rescoring of peptide-spectrum matches with Percolator: semi-supervised SVM FDR estimation for improved sensitivity Pipelines & Workflow Elements Runnable Workflow Darwin Pgdb Proteogenomics database generation from RNA-seq, variants, and reference proteomes for custom protein search databases. Pipelines & Workflow Elements Runnable Workflow Darwin Phageannotator Automated annotation of bacteriophage genomes from metagenomic assemblies using geNomad and CheckV. Pipelines & Workflow Elements Runnable Workflow Darwin Phaseimpute Haplotype phasing and genotype imputation from low-coverage WGS using GLIMPSE2 or BEAGLE Pipelines & Workflow Elements Runnable Workflow Darwin Phyloplace Phylogenetic placement of query sequences onto a reference tree using EPA-ng or pplacer for outbreak and surveillance analysis Pipelines & Workflow Elements Runnable Workflow Darwin Phyloseq Tool R-based microbiome data handling and analysis with phyloseq: OTU/ASV normalization, ordination, diversity testing, and differential abundance Pipelines & Workflow Elements Runnable Workflow Darwin Primateai3d Variant effect predictor leveraging primate evolutionary constraint and 3D protein structure. Pipelines & Workflow Elements Runnable Workflow Darwin Prostt5 Protein language model translating between amino acid sequence and 3Di structure tokens. Pipelines & Workflow Elements Runnable Workflow Darwin Pydeseq2 Tool Rust-native DESeq2 reimplementation for differential expression. Deterministic via research data artifact analysis element. Pipelines & Workflow Elements Runnable expression matrices thelovelab/DESeq2 | 465 stars Darwin Pyprophet Tool Semi-supervised learning FDR estimation for DIA proteomics with PyProphet: score-based filtering and multi-run alignment of OpenSWATH results Pipelines & Workflow Elements Runnable Workflow Darwin Qiime2 Tool Comprehensive microbiome analysis with QIIME 2: DADA2 denoising, ASV table construction, diversity metrics, and taxonomic classification Pipelines & Workflow Elements Runnable Workflow Darwin Radseq Restriction site-associated DNA sequencing analysis for population genetics using Stacks. Pipelines & Workflow Elements Runnable Workflow Darwin Readsimulator Simulate short and long sequencing reads from reference genomes using ART and NanoSim for benchmarking. Pipelines & Workflow Elements Runnable Workflow Darwin Rfdiffusion Diffusion-based de novo protein design, motif scaffolding, and partial diffusion for guided design. Pipelines & Workflow Elements Runnable Workflow Darwin Rhofold Deep learning model for end-to-end prediction of 3D RNA tertiary structures from sequence. Pipelines & Workflow Elements Runnable Workflow Darwin Rinalmo Large RNA language model with 650M parameters pre-trained on 36M ncRNA sequences. Pipelines & Workflow Elements Runnable Workflow Darwin RNA Fm RNA foundation model pre-trained on 23M non-coding RNA sequences for structure and function prediction. Pipelines & Workflow Elements Runnable Workflow Darwin RNA-seq Complete RNA-seq analysis: QC, trimming, alignment, quantification, and differential expression Pipelines & Workflow Elements Runnable Workflow Darwin Rnavar Variant calling from RNA-seq data using GATK4 best practices including alignment, BQSR, and HaplotypeCaller. Pipelines & Workflow Elements Runnable Workflow Darwin Rosettafold Three-track neural network for accurate protein structure prediction using evolutionary information. Pipelines & Workflow Elements Runnable Workflow Darwin Sage Tool Fast and memory-efficient proteomics database search with Sage: fragmentation-based peptide identification with FDR control and TMT quantification Pipelines & Workflow Elements Runnable Workflow Darwin Scanpy Workspace Rust-native single-cell analysis workspace. Preprocessing, normalization, PCA, UMAP, Leiden clustering. Pipelines & Workflow Elements Runnable sequencing reads scverse/scanpy | 2,497 stars Darwin Scdownstream Downstream single-cell RNA-seq analysis including clustering, annotation, trajectory inference, and cell-cell communication. Pipelines & Workflow Elements Runnable Workflow Darwin Scfoundation 100M parameter pre-trained model on 50M+ single-cell profiles with 19,264 gene vocabulary. Pipelines & Workflow Elements Runnable Workflow Darwin scGPT Generative pre-trained transformer for single-cell transcriptomics with cell type annotation and perturbation prediction. Pipelines & Workflow Elements Runnable Workflow bowang-lab/scGPT | 1,589 stars Darwin Scvelo Tool RNA velocity estimation with scVelo: dynamical modeling of spliced/unspliced ratios for cell state prediction Pipelines & Workflow Elements Runnable Workflow Darwin Sei Model Sequence-expression integrated model predicting chromatin profiles and gene expression from sequence. Pipelines & Workflow Elements Runnable Workflow Darwin Seurat Workspace Comprehensive single-cell RNA-seq analysis with Seurat: QC filtering, normalization, dimensionality reduction, clustering, and marker identification Pipelines & Workflow Elements Runnable Workflow satijalab/seurat | 2,759 stars Darwin Signac Tool Single-cell chromatin accessibility analysis with Signac: peak calling, chromatin remodeling, transcription factor motif analysis, and multi-modal integration Pipelines & Workflow Elements Runnable Workflow satijalab/seurat | 2,759 stars Darwin Skyline Tool Targeted mass spectrometry data analysis with Skyline: SRM/MRM transition optimization, peak integration, and quantitative reporting Pipelines & Workflow Elements Runnable Workflow Darwin Slingshot Tool Lineage and pseudotime inference with Slingshot: graph-based trajectory detection in single-cell data Pipelines & Workflow Elements Runnable Workflow Darwin Smrnaseq Small RNA-seq analysis including QC, trimming, miRNA quantification, novel miRNA discovery, and differential expression. Pipelines & Workflow Elements Runnable Workflow Darwin Snapatac2 Tool Scalable single-cell ATAC-seq analysis with SnapATAC2: spectral embedding, peak calling, TF motif scanning, and multi-sample integration Pipelines & Workflow Elements Runnable aligned sequencing reads Darwin Spliceai Deep residual network predicting splicing effects of genetic variants from pre-mRNA sequence. Pipelines & Workflow Elements Runnable Workflow Darwin Spotrna Single sequence-based RNA secondary structure prediction including pseudoknots using transfer learning. Pipelines & Workflow Elements Runnable Workflow Darwin Squidpy Tool Spatial molecular data analysis with Squidpy: spatial statistics, neighborhood enrichment, co-occurrence, and ligand-receptor interactions Pipelines & Workflow Elements Runnable Workflow Darwin Starsolo Single-cell RNA-seq quantification using STARsolo: barcode demultiplexing, alignment, and count matrix generation Pipelines & Workflow Elements Runnable Workflow alexdobin/STAR | 2,216 stars Darwin Tangram Deep learning method mapping single-cell transcriptomics to spatial coordinates. Pipelines & Workflow Elements Runnable Workflow Darwin Taxpasta Standardise and merge taxonomic profiles from multiple classifiers into unified abundance tables. Pipelines & Workflow Elements Runnable Workflow Darwin Thermorawfileparser Tool Conversion of Thermo Fisher RAW mass spectrometry files to open formats (mzML, MGF, mzXML) using ThermoRawFileParser Pipelines & Workflow Elements Runnable Workflow Darwin Totalvi Variational autoencoder for CITE-seq joint RNA and protein expression analysis. Pipelines & Workflow Elements Runnable Workflow Darwin Uce Zero-shot universal cell embedding model mapping cells from any species to a unified latent space. Pipelines & Workflow Elements Runnable Workflow Darwinomics Cgt Pipeline Allogeneic Cell Therapy Comparability End-to-end allogeneic cell therapy comparability pipeline. Pipelines & Workflow Elements Available Workflow Darwinomics Cgt Pipeline Autologous Cell Therapy Release End-to-end autologous cell therapy release-readiness pipeline. Pipelines & Workflow Elements Available Workflow Darwinomics Cgt Pipeline Ex Vivo Gene Editing Safety End-to-end ex vivo gene-editing safety evidence pipeline. Pipelines & Workflow Elements Available Workflow Darwinomics Cgt Pipeline In Vivo Gene Therapy Cmc End-to-end in vivo gene therapy CMC evidence package pipeline. Pipelines & Workflow Elements Available Workflow Darwinomics Cgt Pipeline Long Term Followup Long-term follow-up harmonization and monitoring pipeline. Pipelines & Workflow Elements Available Workflow Darwinomics Cgt Pipeline Regulatory Package Regulatory evidence package assembly pipeline for CGT programs. Pipelines & Workflow Elements Available Workflow Darwinomics Design Run Orchestrator Darwinomics Design Run Orchestrator coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Darwinomics Engine The deterministic execution layer. Takes approved execution plans from the agent and runs them step by step. Does NOT decide what to run — the agent decides. The engine only executes. Pipelines & Workflow Elements Runnable Workflow Darwinomics Proto Binder Design Bindcraft Darwinomics Proto Binder Design Bindcraft applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow Darwinomics Proto Binder Design Freebindcraft Darwinomics Proto Binder Design Freebindcraft applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow Darwinomics Proto Binder Design Germinal Darwinomics Proto Binder Design Germinal applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow Document To Module Contract pipeline document to module analysis element Pipelines & Workflow Elements Runnable Workflow Drop Pipeline Drop Pipeline coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Drug Discovery Pipeline Drug Discovery Pipeline supports molecular design or docking analysis with structured inputs, scored outputs, and provenance for review. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Esmfold Fast structure prediction using ESMFold. Pipelines & Workflow Elements Runnable protein or structure data facebookresearch/esm | 4,140 stars Filter Variants Filter Variants supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Pipelines & Workflow Elements Runnable sequencing reads Fluorescence Cell Count Fluorescence Cell Count processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable image or spatial data GPU WGS WGS pipeline using NVIDIA Parabricks for 30-50x faster alignment and variant calling. Pipelines & Workflow Elements Runnable Workflow Hi C Hi-C data processing using HiC-Pro. Pipelines & Workflow Elements Runnable sequencing reads Hic Hi-C chromatin conformation capture pipeline. Pipelines & Workflow Elements Runnable sequencing reads Inverse Folding Design Inverse Folding Design applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable protein or structure data Longread Isoseq Longread Isoseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Longread Nanopore Long-read Nanopore alignment and variant calling. Pipelines & Workflow Elements Runnable Workflow Metagenomics Bracken Abundance estimation from Kraken2 output. Pipelines & Workflow Elements Runnable sequencing reads Metagenomics Kraken2 Taxonomic classification using Kraken2. Identifies organisms in mixed microbial samples. Pipelines & Workflow Elements Runnable sequencing reads Metagenomics Viral Viral classification from metagenomic data. Pipelines & Workflow Elements Runnable Workflow Methylation Bsseq WGBS methylation analysis with Bismark. Pipelines & Workflow Elements Runnable aligned sequencing reads Methylation Nanopore Methylation calling from Oxford Nanopore data. Pipelines & Workflow Elements Runnable aligned sequencing reads Methylation Rrbs RRBS methylation analysis for CpG-rich regions. Pipelines & Workflow Elements Runnable aligned sequencing reads Methylation Wgbs WGBS methylation analysis using Bismark for bisulfite alignment and methylation calling. Pipelines & Workflow Elements Runnable aligned sequencing reads Microscopy Segmentation Benchmark Microscopy Segmentation Benchmark processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable image or spatial data Msa Structure Prediction Msa Structure Prediction applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable sequence data Msa Structure Prediction Pipeline bionemo msa structure prediction pipeline Pipelines & Workflow Elements Runnable sequence data NVIDIA-BioNeMo/bionemo-recipes | 806 stars Nf Core Bacmodel Nf Core Bacmodel coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/bacmodel | 2 stars Nf Core Dartseq Nf Core Dartseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/dartseq | 0 stars Nf Core Epigenomesegmentation Nf Core Epigenomesegmentation processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable Workflow nf-core/epigenomesegmentation | 1 stars Nf Core Genephylomodeler Nf Core Genephylomodeler coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/genephylomodeler | 1 stars Nf Core Hic Nf Core Hic coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable expression matrices nf-core/hic | 110 stars Nf Core Mag Nf Core Mag supports microbiome or metagenomic analysis so taxonomic, assembly, or quality results can be regenerated. Pipelines & Workflow Elements Runnable Workflow nf-core/mag | 306 stars Nf Core Mspepid Nf Core Mspepid coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/mspepid | 3 stars Nf Core Ncrnannotator Nf Core Ncrnannotator coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/ncrnannotator | 1 stars Nf Core Spatialaxe Nf Core Spatialaxe processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable Workflow nf-core/spatialaxe | 39 stars Nf Core Ssds Nf Core Ssds coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/ssds | 1 stars Nf Core Vipr Nf Core Vipr coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/vipr | 15 stars Nfcore Abotyper Nfcore Abotyper coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/abotyper | 4 stars Nfcore Airrflow Nfcore Airrflow coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/airrflow | 80 stars Nfcore Alleleexpression Nfcore Alleleexpression handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/alleleexpression | 2 stars Nfcore Ampliseq Nfcore Ampliseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/ampliseq | 252 stars Nfcore ATAC-seq Nfcore ATAC-seq handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/atacseq | 227 stars Nfcore Bacass Nfcore Bacass coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/bacass | 89 stars Nfcore Bactmap Nfcore Bactmap coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/bactmap | 67 stars Nfcore Bamtofastq Nfcore Bamtofastq handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable Workflow nf-core/bamtofastq | 32 stars Nfcore Cageseq Nfcore Cageseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/cageseq | 11 stars Nfcore Callingcards Nfcore Callingcards coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/callingcards | 5 stars Nfcore Cellpainting Nfcore Cellpainting coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/cellpainting | 9 stars Nfcore ChIP-seq Nfcore ChIP-seq handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/chipseq | 241 stars Nfcore Circdna Nfcore Circdna coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/circdna | 35 stars Nfcore Circrna Nfcore Circrna coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/circrna | 61 stars Nfcore Clipseq Nfcore Clipseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/clipseq | 24 stars Nfcore Coproid Nfcore Coproid coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/coproid | 13 stars Nfcore Createpanelrefs Nfcore Createpanelrefs coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/createpanelrefs | 11 stars Nfcore Createtaxdb Nfcore Createtaxdb coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/createtaxdb | 21 stars Nfcore Crisprseq Nfcore Crisprseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/crisprseq | 61 stars Nfcore Crisprvar Nfcore Crisprvar coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/crisprvar | 5 stars Nfcore Cutandrun Nfcore Cutandrun coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/cutandrun | 112 stars Nfcore Datasync Nfcore Datasync coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/datasync | 10 stars Nfcore Ddamsproteomics Nfcore Ddamsproteomics coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/ddamsproteomics | 4 stars Nfcore Deepmodeloptim Nfcore Deepmodeloptim coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/deepmodeloptim | 31 stars Nfcore Deepmutscan Nfcore Deepmutscan coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/deepmutscan | 5 stars Nfcore Deepvariant Nfcore Deepvariant handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/deepvariant | 41 stars Nfcore Demultiplex Nfcore Demultiplex coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/demultiplex | 55 stars Nfcore Denovohybrid Nfcore Denovohybrid coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/denovohybrid | 9 stars Nfcore Denovotranscript Nfcore Denovotranscript coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/denovotranscript | 25 stars Nfcore Detaxizer Nfcore Detaxizer coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/detaxizer | 24 stars Nfcore Diaproteomics Nfcore Diaproteomics coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/diaproteomics | 21 stars Nfcore Differentialabundance Nfcore Differentialabundance supports differential analysis from expression matrices, preserving effect sizes, test statistics, and result tables for comparison. Pipelines & Workflow Elements Runnable Workflow nf-core/differentialabundance | 94 stars Nfcore Diseasemodulediscovery Nfcore Diseasemodulediscovery coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/diseasemodulediscovery | 5 stars Nfcore Drop Nfcore Drop coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/drop | 12 stars Nfcore Drugresponseeval Nfcore Drugresponseeval supports molecular design or docking analysis with structured inputs, scored outputs, and provenance for review. Pipelines & Workflow Elements Runnable Workflow nf-core/drugresponseeval | 29 stars Nfcore Dualrnaseq Nfcore Dualrnaseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/dualrnaseq | 25 stars Nfcore Eager Nfcore Eager coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/eager | 208 stars Nfcore Epitopeprediction Nfcore Epitopeprediction coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/epitopeprediction | 52 stars Nfcore Evexplorer Nfcore Evexplorer coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/evexplorer | 1 stars Nfcore Fastqrepair Nfcore Fastqrepair coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/fastqrepair | 9 stars Nfcore Fastquorum Nfcore Fastquorum coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/fastquorum | 28 stars Nfcore Fetchngs Nfcore Fetchngs coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/fetchngs | 196 stars Nfcore Funcprofiler Nfcore Funcprofiler coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/funcprofiler | 2 stars Nfcore Funcscan Nfcore Funcscan coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/funcscan | 113 stars Nfcore Genomeannotator Nfcore Genomeannotator coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/genomeannotator | 37 stars Nfcore Genomeassembler Nfcore Genomeassembler coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable sequencing reads nf-core/genomeassembler | 33 stars Nfcore Genomeqc Nfcore Genomeqc summarizes sequencing or run-quality metrics so reviewers can check whether preprocessing and input quality match the reported analysis. Pipelines & Workflow Elements Runnable Workflow nf-core/genomeqc | 22 stars Nfcore Genomeskim Nfcore Genomeskim coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/genomeskim | 4 stars Nfcore Genomicrelatedness Nfcore Genomicrelatedness coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/genomicrelatedness | 2 stars Nfcore Gwas Nfcore Gwas coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/gwas | 28 stars Nfcore Hadge Nfcore Hadge coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/hadge | 26 stars Nfcore Hgtseq Nfcore Hgtseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/hgtseq | 27 stars Nfcore Hic Nfcore Hic coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/hic | 110 stars Nfcore Hicar Nfcore Hicar coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/hicar | 12 stars Nfcore Hlatyping Nfcore Hlatyping coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/hlatyping | 81 stars Nfcore Imcyto Nfcore Imcyto coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/imcyto | 26 stars Nfcore Isoseq Nfcore Isoseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/isoseq | 54 stars Nfcore Kmermaid Nfcore Kmermaid coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/kmermaid | 23 stars Nfcore Lncpipe Nfcore Lncpipe coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/lncpipe | 34 stars Nfcore Longraredisease Nfcore Longraredisease coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/longraredisease | 11 stars Nfcore Lsmquant Nfcore Lsmquant handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/lsmquant | 6 stars Nfcore Mag Nfcore Mag supports microbiome or metagenomic analysis so taxonomic, assembly, or quality results can be regenerated. Pipelines & Workflow Elements Runnable Workflow nf-core/mag | 306 stars Nfcore Magmap Nfcore Magmap supports microbiome or metagenomic analysis so taxonomic, assembly, or quality results can be regenerated. Pipelines & Workflow Elements Runnable Workflow nf-core/magmap | 10 stars Nfcore Marsseq Nfcore Marsseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/marsseq | 9 stars Nfcore Mcmicro Nfcore Mcmicro coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/mcmicro | 32 stars Nfcore Meerpipe Nfcore Meerpipe coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/meerpipe | 11 stars Nfcore Metaboigniter Nfcore Metaboigniter coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/metaboigniter | 24 stars Nfcore Metapep Nfcore Metapep coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/metapep | 12 stars Nfcore Metatdenovo Nfcore Metatdenovo coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/metatdenovo | 34 stars Nfcore Methylarray Nfcore Methylarray handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/methylarray | 7 stars Nfcore Methylong Nfcore Methylong handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/methylong | 24 stars Nfcore Methylseq Nfcore Methylseq handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/methylseq | 193 stars Nfcore Mhcquant Nfcore Mhcquant handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/mhcquant | 48 stars Nfcore Mitodetect Nfcore Mitodetect coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/mitodetect | 7 stars Nfcore Mnaseseq Nfcore Mnaseseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/mnaseseq | 13 stars Nfcore Molkart Nfcore Molkart coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/molkart | 13 stars Nfcore Multiometools Nfcore Multiometools coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Nfcore Multiplesequencealign Nfcore Multiplesequencealign handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable sequencing reads nf-core/multiplesequencealign | 41 stars Nfcore Nanoseq Nfcore Nanoseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/nanoseq | 227 stars Nfcore Nanostring Nfcore Nanostring coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/nanostring | 18 stars Nfcore Nascent Nfcore Nascent coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/nascent | 23 stars Nfcore Omicsgenetraitassociation Nfcore Omicsgenetraitassociation coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/omicsgenetraitassociation | 11 stars Nfcore Oncoanalyser Nfcore Oncoanalyser coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/oncoanalyser | 116 stars Nfcore Pacsomatic Nfcore Pacsomatic coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/pacsomatic | 2 stars Nfcore Pacvar Nfcore Pacvar coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/pacvar | 16 stars Nfcore Pairgenomealign Nfcore Pairgenomealign handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable sequencing reads nf-core/pairgenomealign | 12 stars Nfcore Pangenome Nfcore Pangenome coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/pangenome | 108 stars Nfcore Panoramaseq Nfcore Panoramaseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/panoramaseq | 0 stars Nfcore Pathogensurveillance Nfcore Pathogensurveillance coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/pathogensurveillance | 61 stars Nfcore Pgdb Nfcore Pgdb coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Nfcore Phageannotator Nfcore Phageannotator coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/phageannotator | 19 stars Nfcore Phaseimpute Nfcore Phaseimpute coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/phaseimpute | 32 stars Nfcore Phyloplace Nfcore Phyloplace coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/phyloplace | 12 stars Nfcore Pixelator Nfcore Pixelator coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/pixelator | 14 stars Nfcore Proteinannotator Nfcore Proteinannotator applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow nf-core/proteinannotator | 13 stars Nfcore Proteinfamilies Nfcore Proteinfamilies applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow nf-core/proteinfamilies | 22 stars Nfcore Proteinfold Nfcore Proteinfold applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow nf-core/proteinfold | 108 stars Nfcore Proteogenomicsdb Nfcore Proteogenomicsdb coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/proteogenomicsdb | 7 stars Nfcore Proteomicslfq Nfcore Proteomicslfq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/proteomicslfq | 37 stars Nfcore Quantms Nfcore Quantms handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/quantms | 41 stars Nfcore Radseq Nfcore Radseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/radseq | 7 stars Nfcore Rangeland Nfcore Rangeland coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/rangeland | 10 stars Nfcore Raredisease Nfcore Raredisease coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/raredisease | 119 stars Nfcore Rarevariantburden Nfcore Rarevariantburden handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/rarevariantburden | 0 stars Nfcore Readsimulator Nfcore Readsimulator coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/readsimulator | 34 stars Nfcore References Nfcore References coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/references | 20 stars Nfcore Reportho Nfcore Reportho coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/reportho | 11 stars Nfcore Ribomsqc Nfcore Ribomsqc summarizes sequencing or run-quality metrics so reviewers can check whether preprocessing and input quality match the reported analysis. Pipelines & Workflow Elements Runnable Workflow nf-core/ribomsqc | 1 stars Nfcore Riboseq Nfcore Riboseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/riboseq | 30 stars Nfcore RNA-seq Nfcore RNA-seq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/rnaseq | 1,322 stars Nfcore Rnadnavar Nfcore Rnadnavar coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/rnadnavar | 13 stars Nfcore Rnafusion Nfcore Rnafusion coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/rnafusion | 174 stars Nfcore Rnasplice Nfcore Rnasplice coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/rnasplice | 68 stars Nfcore Rnavar Nfcore Rnavar coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/rnavar | 61 stars Nfcore Sammyseq Nfcore Sammyseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/sammyseq | 4 stars Nfcore Sarek Nfcore Sarek coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/sarek | 578 stars Nfcore Scdownstream Nfcore Scdownstream coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/scdownstream | 109 stars Nfcore Scflow Nfcore Scflow coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/scflow | 26 stars Nfcore Scnanoseq Nfcore Scnanoseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/scnanoseq | 55 stars Nfcore scRNA-seq Nfcore scRNA-seq supports single-cell analysis, annotation, or embedding workflows with reproducible matrix and metadata handling. Pipelines & Workflow Elements Runnable Workflow nf-core/scrnaseq | 336 stars Nfcore Seqinspector Nfcore Seqinspector coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/seqinspector | 25 stars Nfcore Seqsubmit Nfcore Seqsubmit coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/seqsubmit | 6 stars Nfcore Slamseq Nfcore Slamseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/slamseq | 10 stars Nfcore Smartseq2 Nfcore Smartseq2 coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/smartseq2 | 17 stars Nfcore Smrnaseq Nfcore Smrnaseq coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/smrnaseq | 100 stars Nfcore Sopa Nfcore Sopa coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/sopa | 18 stars Nfcore Spatialvi Nfcore Spatialvi processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable Workflow nf-core/spatialvi | 76 stars Nfcore Spatialxe Nfcore Spatialxe processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable Workflow Nfcore Spinningjenny Nfcore Spinningjenny coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/spinningjenny | 4 stars Nfcore Stableexpression Nfcore Stableexpression handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/stableexpression | 9 stars Nfcore Taxpasta Nfcore Taxpasta coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Nfcore Taxprofiler Nfcore Taxprofiler coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/taxprofiler | 188 stars Nfcore Tbanalyzer Nfcore Tbanalyzer coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/tbanalyzer | 13 stars Nfcore Tfactivity Nfcore Tfactivity coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/tfactivity | 12 stars Nfcore Troughgraph Nfcore Troughgraph coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/troughgraph | 2 stars Nfcore Tumourevo Nfcore Tumourevo coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/tumourevo | 22 stars Nfcore Variantbenchmarking Nfcore Variantbenchmarking handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/variantbenchmarking | 50 stars Nfcore Variantcatalogue Pileup-based variant calling for research data artifact. Groups reads by genomic position, counts base frequencies, calls the reference as the most common base, and emits research data artifact records for minority alleles exceeding 20%... Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/variantcatalogue | 13 stars Nfcore Variantprioritization Nfcore Variantprioritization handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Pipelines & Workflow Elements Runnable aligned sequencing reads nf-core/variantprioritization | 15 stars Nfcore Viralintegration Nfcore Viralintegration coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/viralintegration | 18 stars Nfcore Viralmetagenome Nfcore Viralmetagenome supports microbiome or metagenomic analysis so taxonomic, assembly, or quality results can be regenerated. Pipelines & Workflow Elements Runnable Workflow nf-core/viralmetagenome | 39 stars Nfcore Viralrecon Nfcore Viralrecon coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow nf-core/viralrecon | 165 stars Promoter Repressor Codesign Promoter Repressor Codesign coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Protein Binder Design Protein Binder Design applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow NVIDIA-BioNeMo/bionemo-recipes | 806 stars Protein Binder Design Protein Binder Design applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Pipelines & Workflow Elements Runnable Workflow Protein Design De novo protein design using RFdiffusion for structure and ProteinMPNN for sequence. Pipelines & Workflow Elements Runnable protein or structure data Proteinmpnn Protein sequence design given a backbone structure. Pipelines & Workflow Elements Runnable protein or structure data Proteomics Dia Proteomics Dia coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow Proteomics Quantification Protein quantification from mass spectrometry data. Pipelines & Workflow Elements Runnable aligned sequencing reads Proto Style Sequence Design pipeline proto style sequence design Pipelines & Workflow Elements Runnable Workflow QC FastQC Run FastQC quality control only. Pipelines & Workflow Elements Runnable sequencing reads s-andrews/FastQC | 602 stars QC Multiqc Aggregate QC reports from multiple samples. Pipelines & Workflow Elements Runnable sequencing reads MultiQC/MultiQC | 1,466 stars QC Only Run QC on sequencing data without alignment. Quick assessment before committing to full analysis. Pipelines & Workflow Elements Runnable sequencing reads Regulatory Variant Scoring Regulatory Variant Scoring supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Pipelines & Workflow Elements Runnable sequence data Rfdiffusion De novo protein design using RFdiffusion. Pipelines & Workflow Elements Runnable Workflow RNA Speed RNA Speed quantifies reads, transcripts, or feature counts so expression-level results can be regenerated and compared. Pipelines & Workflow Elements Runnable Workflow RNA-seq Standard RNA-seq analysis: QC -> trimming -> alignment -> quantification -> differential expression. The most common bioinformatics pipeline. Pipelines & Workflow Elements Runnable sequencing reads RNA-seq Alevin Single-cell RNA-seq quantification using alevin/Salmon. Pipelines & Workflow Elements Runnable sequencing reads COMBINE-lab/salmon | 901 stars RNA-seq De Edger Research-certified RNA-seq differential-expression pipeline wrapping the certified Rust-native edgeR 4.10.1 GLM quasi-likelihood fixture executor. Pipelines & Workflow Elements Runnable expression matrices RNA-seq De Limma Research-certified RNA-seq differential-expression pipeline wrapping the certified Rust-native limma 3.68.4 plus edgeR 4.10.1 voom fixture executor. Pipelines & Workflow Elements Runnable expression matrices RNA-seq Hisat2 RNA-seq using HISAT2 instead of STAR. Uses ~8GB RAM instead of ~32GB. Good for memory-constrained environments. Pipelines & Workflow Elements Runnable sequencing reads DaehwanKimLab/hisat2 | 539 stars RNA-seq Salmon RNA-seq quantification using Salmon instead of STAR+featureCounts. Faster when you only need gene-level counts and don't need BAM files. Pipelines & Workflow Elements Runnable aligned sequencing reads COMBINE-lab/salmon | 901 stars RNA-seq Salmon Quant RNA-seq using Salmon quasi-mapping for fast quantification without full alignment. Pipelines & Workflow Elements Runnable aligned sequencing reads COMBINE-lab/salmon | 901 stars RNA-seq Star Featurecounts Standard RNA-seq using STAR alignment and featureCounts quantification. Pipelines & Workflow Elements Runnable sequencing reads alexdobin/STAR | 2,216 stars RNA-seq Star Salmon RNA-seq using STAR alignment followed by Salmon quantification and DESeq2 differential expression. Pipelines & Workflow Elements Runnable sequencing reads alexdobin/STAR | 2,216 stars Sarek Germline Germline variant calling using GATK Best Practices: alignment -> mark duplicates -> BQSR -> HaplotypeCaller -> annotation. Pipelines & Workflow Elements Runnable Workflow Sarek Germline Deepvariant Germline variant calling using DeepVariant for higher accuracy. Pipelines & Workflow Elements Runnable aligned sequencing reads google/deepvariant | 3,740 stars Sarek Germline Dv Germline variant calling using GPU-accelerated DeepVariant instead of GATK. More accurate but requires GPU. Pipelines & Workflow Elements Runnable Workflow Sarek Germline GATK4 Germline variant calling using GATK4 HaplotypeCaller. Pipelines & Workflow Elements Runnable Workflow broadinstitute/gatk | 1,970 stars Sarek Somatic Somatic variant calling using GATK Mutect2 for tumor-normal pairs. Pipelines & Workflow Elements Runnable Workflow Sarek Somatic Manta Structural variant calling using Manta. Pipelines & Workflow Elements Runnable Workflow Sarek Somatic Mutect2 Somatic variant calling with Mutect2 for cancer genomics. Pipelines & Workflow Elements Runnable aligned sequencing reads Sarek Somatic Strelka Somatic variant calling using Strelka2. Pipelines & Workflow Elements Runnable aligned sequencing reads Singlecell scRNA-seq preprocessing, dimensionality reduction, and clustering. For 10x Genomics data. Pipelines & Workflow Elements Runnable sequencing reads Singlecell Atac scATAC-seq analysis for mapping chromatin accessibility at single-cell resolution. Pipelines & Workflow Elements Runnable aligned sequencing reads Singlecell Multiome Singlecell Multiome supports single-cell analysis, annotation, or embedding workflows with reproducible matrix and metadata handling. Pipelines & Workflow Elements Runnable sequencing reads Singlecell RNA-seq Single-cell RNA-seq with 10x Genomics CellRanger. Pipelines & Workflow Elements Runnable sequencing reads Singlecell RNA-seq Scanpy Single-cell preprocessing, normalization, UMAP, and Leiden clustering. Pipelines & Workflow Elements Runnable sequencing reads scverse/scanpy | 2,497 stars Singlecell RNA-seq scGPT Single-cell RNA-seq with scGPT cell type annotation. Pipelines & Workflow Elements Runnable sequencing reads bowang-lab/scGPT | 1,589 stars Singlecell scGPT scRNA-seq with automatic cell type annotation using scGPT foundation model. Pipelines & Workflow Elements Runnable sequencing reads bowang-lab/scGPT | 1,589 stars Singlecell Vdj Single-cell V(D)J immune repertoire profiling. Pipelines & Workflow Elements Runnable sequencing reads Smfish Count Smfish Count processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Pipelines & Workflow Elements Runnable image or spatial data Somatic Variant Calling Tumor-normal paired somatic variant calling using GATK Mutect2. For cancer genomics. Pipelines & Workflow Elements Runnable aligned sequencing reads Structural Biology Predicts 3D protein structure from amino acid sequence using AlphaFold2. Pipelines & Workflow Elements Runnable Workflow Structural Biology Complex Predicts structures of protein-protein and protein-nucleic acid complexes. Pipelines & Workflow Elements Runnable Workflow Structural Biology Fast Fast protein structure prediction using ESMFold. Less accurate than AlphaFold2 but 6x faster. Pipelines & Workflow Elements Runnable Workflow Trim Only Just adapter trimming, no alignment. Pipelines & Workflow Elements Runnable sequencing reads Variant Annotation Annotate existing VCF files with gene names, functional consequences, and population frequencies. Pipelines & Workflow Elements Runnable aligned sequencing reads Virtual Screening Virtual Screening coordinates a multi-step computational workflow with captured inputs, execution context, and output artifacts for review. Pipelines & Workflow Elements Runnable Workflow WES WES variant calling. Same as WGS but optimized for exome capture data. Pipelines & Workflow Elements Runnable sequencing reads WES GATK4 GATK4 best practices for WES. Pipelines & Workflow Elements Runnable sequencing reads broadinstitute/gatk | 1,970 stars WGS WGS variant calling with BWA-MEM2 alignment, duplicate marking, BQSR, and GATK HaplotypeCaller. Pipelines & Workflow Elements Runnable sequencing reads WGS GATK4 GATK4 best practices pipeline for WGS. Pipelines & Workflow Elements Runnable sequencing reads broadinstitute/gatk | 1,970 stars