Nextflow Modules
Showing module(s) with keyword "protein"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bcftools/csq | annotation gff gff3 protein functional vcf bcf bcftools | bcftools Haplotype-aware consequence caller |
| nf-core/blast/blastp | fasta blast blastp protein | BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database |
| nf-core/caalm/caalm | cazyme annotation protein language model deep learning classification | Annotates carbohydrate-active enzyme (CAZyme) families from protein sequences using protein language model (ESM) embeddings and FAISS-based nearest-neighbour search. Performs three-level hierarchical classification: binary CAZyme detection (Level 0), CAZy class assignment (Level 1), and CAZy family assignment (Level 2). |
| nf-core/cdhit/cdhit | cluster protein alignment fasta | Cluster protein sequences using sequence similarity |
| nf-core/clusty | cluster network contig scaffold alignment protein | Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects. |
| nf-core/deeptmhmm | transmembrane protein classification | A Deep Learning Model for Transmembrane Topology Prediction and Classification |
| nf-core/diamond/deepclust | clustering protein diamond deepclust proteomics | Fast graph-based protein sequence clustering using DIAMOND deepclust |
| nf-core/diamond/linclust | clustering protein diamond linclust proteomics | Fast protein sequence clustering using a greedy incremental approach |
| nf-core/dssp/mkdssp | protein secondary structure structural bioinformatics dssp mkdssp | Calculates secondary structure assignments from PDB files using mkdssp (DSSP). DSSP is a standard tool for assigning secondary structure to amino acids in protein structures. |
| nf-core/foldcomp/compress | protein structure compression | Efficient compression tool for protein structures |
| nf-core/foldcomp/decompress | protein structure compression | Decompression tool for foldcomp compressed structures |
| nf-core/foldseek/createdb | protein structure comparisons | Create a database from protein structures |
| nf-core/foldseek/easysearch | protein structure comparisons | Search for protein structural hits against a foldseek database of protein structures |
| nf-core/fungtion/downloadmodels | fungal effector protein prediction language model deep learning model download | Downloads the pretrained ESM-1b weights (esm1b_t33_650M_UR50S.pt) that fungtion uses for fungal effector prediction into a local models/ directory via `fungtion setup-models`. The downloaded directory is used as input to the FUNGTION_FUNGTION prediction module. |
| nf-core/fungtion/fungtion | fungal effector protein prediction language model deep learning svm classification | Predicts fungal effector proteins from protein FASTA sequences using ESM-1b protein language model embeddings and R-based SVM models. Optionally produces similarity-network and relationship-tree visualizations and an HTML report for predicted effectors. Requires the pretrained ESM-1b weights from FUNGTION_DOWNLOADMODELS as input. |
| nf-core/interproscan | annotation fasta protein dna interproscan | Produces protein annotations and predictions from an amino acids FASTA file |
| nf-core/localcdsearch/annotate | cdd rpsblast rpsbproc protein domain annotation | A command-line tool for local protein domain annotation using NCBI's Conserved Domain Database (CDD) |
| nf-core/localcdsearch/download | cdd rpsblast rpsbproc prot |