This repository contains a list of Nextflow pipelines.
| Name | Repository | Description | Run in Nextflow with provided test data |
|---|---|---|---|
| iridanextexample | https://github.com/phac-nml/iridanextexample | A pipeline to help integrate Nextflow with IRIDA Next. | nextflow run phac-nml/iridanextexample -profile test,docker --outdir results |
| Mikrokondo | https://github.com/phac-nml/mikrokondo | A simple pipeline for bacterial assembly and quality control. | nextflow run phac-nml/mikrokondo -profile test,docker --outdir results |
| SNVPhyl | https://github.com/phac-nml/snvphylnfc | A pipeline for whole-genome phylogenetic analysis | nextflow run phac-nml/snvphylnfc -profile test,docker --outdir results |
| fetchdatairidanext | https://github.com/phac-nml/fetchdatairidanext | A pipeline for downloading reads from NCBI. | nextflow run phac-nml/fetchdatairidanext -profile test,docker --outdir results |
| speciesabundance | https://github.com/phac-nml/speciesabundance | Estimate the relative abundance of sequence reads originating from different species in a sample. | nextflow run phac-nml/speciesabundance -profile test,docker --outdir results |
| gasclustering | https://github.com/phac-nml/gasclustering | Clusters provided wg/cgMLST profiles for samples (in JSON format) and provides cluster addresses and a visualization of the dendrogram + metadata. | nextflow run phac-nml/gasclustering -profile test,docker --outdir results |
| gasnomenclature | https://github.com/phac-nml/gasnomenclature | Assigns new wg/cgMLST-derived cluster addresses to samples within the context of previously defined cluster addresses. | nextflow run phac-nml/gasnomenclature -profile test,docker --outdir results |
| staramrnf | https://github.com/phac-nml/staramrnf | Identifies AMR from passed assembled genomes using the StarAMR software. | nextflow run phac-nml/staramrnf -profile test,docker --outdir results |
| arboratornf | https://github.com/phac-nml/arboratornf | Groups samples by provided metadata values and provides summary statistics of wg/cgMLST allelic distances and metadata values. | nextflow run phac-nml/arboratornf -profile test,docker --outdir results |
| fastmatchirida | https://github.com/phac-nml/fastmatchirida | Reports wgMLST distances between selected query samples and a selected set of reference samples. | nextflow run phac-nml/fastmatchirida -profile test,docker --outdir results |
To develop a new pipeline, please refer to the Pipeline standards guide.
Text in this repository is licensed under the Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ license. Licenses for each pipeline are specific to the respective repositories.