Template repository for setting up new Nextflow pipelines
This template has been informed by many other Nextflow pipelines and templates. Some are much more advanced than this template. Please see:
tower.nf allows GUI tracking of workflow progress Set it up using the instructions here
[Describe here what this pipeline does]
This pipeline can be run using each of the following container methods
| Method | Instructions |
|---|---|
| Singularity | docs.syslabs.io |
| Docker | docs.docker.com |
| Conda | docs.conda.io |
sudo singularity build singularity/pipeline Singularity
Then as the profile singularity specifies container = 'singularity/pipeline' use the following to execute:
nextflow run main.nf -profile singularity
docker build . -t pipeline-image
Then as the profile docker specifies container = 'pipeline-image:latest' use the following to execute:
nextflow run main.nf -profile docker
Create a conda definition yaml file eg. here
nextflow run main.nf -profile conda
Call the pipeline directly
nextflow run main.nf
Run with all the frills
bash scripts/run-w-frills <params-file> <profile name from nextflow.config>
Example
bash scripts/run-w-frills example_parameters.yml standard