Nextflow Modules
Showing 2,059 module(s)
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/spmergeannotations | genomics gff merge combine | This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files. |
| nf-core/agat/spstatistics | genome gff gtf statistics | Provides different type of statistics in text format from a GFF/GTF annotation file |
| nf-core/agat/sqstatbasic | genome gff gtf statistics | Provides basic statistics in text format from a GFF/GTF annotation file |
| nf-core/agrvate | fasta virulence Staphylococcus aureus | Rapid identification of Staphylococcus aureus agr locus type and agr operon variants |
| nf-core/ale | reference-independent assembly evaluation | ALE: assembly likelihood estimator. |
| nf-core/alignoth | genomics alignment visualization pileup plotting | Creating alignment plots from bam files |
| nf-core/allelecounter | allele count coverage | Generates a count of coverage of alleles |
| nf-core/ampcombi | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir DRAMP | A tool to parse and summarise results from antimicrobial peptides tools and present functional classification. |
| nf-core/ampcombi2/cluster | antimicrobial peptides amps parsing reporting align clustering mmseqs2 | A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster. |
| nf-core/ampcombi2/complete | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP | A submodule that merges all output summary tables from ampcombi/parsetables in one summary file. |
| nf-core/ampcombi2/parsetables | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP MMseqs2 InterProScan | A submodule that parses and standardizes the results from various antimicrobial peptide identification tools. |
| nf-core/ampir | ampir amp antimicrobial peptide prediction | A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs. |
| nf-core/amplify/predict | antimicrobial peptides AMPs prediction model | AMPlify is an attentive deep learning model for antimicrobial peptide prediction. |
| nf-core/amps | malt MaltExtract HOPS amps alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome authentication damage edit distance post Post-processing visualisation | Post-processing script of the MaltExtract component of the HOPS package |
| nf-core/amrfinderplus/run | bacteria fasta antibiotic resistance | Identify antimicrobial r |