This repository contains a list of Nextflow pipelines.

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
iridanextexample2	https://github.com/phac-nml/iridanextexample2	An example pipeline for running on IRIDA-Next with nf-schema.	nextflow run phac-nml/iridanextexample2 -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
metadatatransformation	https://github.com/phac-nml/metadatatransformation	Transforms metadata in various ways for use in IRIDA Next.	nextflow run phac-nml/metadatatransformation -profile test,docker --outdir results
measeq	https://github.com/phac-nml/measeq	Measles Sequence Analysis and Automation.	nextflow run phac-nml/measeq -profile test,docker --outdir results
typingQC	https://github.com/phac-nml/typingQC	Genotyping Quality Control (typingQC).	nextflow run phac-nml/typingQC -profile test,docker --outdir results
submitdatairidanext	https://github.com/phac-nml/submitdatairidanext	Pipeline for submitting data to INSDC databases for IRIDA Next.	nextflow run phac-nml/submitdatairidanext -profile test,docker --outdir results
cditoxins	https://github.com/phac-nml/cditoxins	Searches for toxin genes in Clostridioides difficile genome assemblies	nextflow run phac-nml/cditoxins -profile test,docker --outdir results

Development

To develop a new pipeline, please refer to the Pipeline standards guide.

License

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.