Installation
Dependencies
The pipeline require only a UNIX system, Nextflow and either Docker, Singularity or conda. Please, for installing these tools refer to their manual.
About NF profiles
Please read more about how to proper select NF profiles to better understand it.
Downloading the pipeline
You can easily get a copy of the pipeline with:
Warning
The pipeline requires a UNIX system, therefore, Windows users may successfully use this pipeline via the Linux subsystem for window. Nextflow team has made available a nice tutorial about this issue.
Downloading docker images
All images can be downloaded on the fly, automatically by nextflow, and this is the recommended way to do it.
If using singularity
Docker and singularity images are downloaded on the fly. Be sure to properly set NXF_SINGULARITY_LIBRARYDIR
env variable to a writable directory if using Singularity. This will make that the downloaded images are reusable through different executions. Read more at: https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
For example, you would:
# prepare env variables
export NXF_SINGULARITY_LIBRARYDIR=<path in your machine> # Set a path to your singularity storage dir
export NXF_SINGULARITY_CACHEDIR=<path in your machine> # Set a path to your singularity cache dir
export SINGULARITY_CACHEDIR=<path in your machine> # Set a path to your singularity cache dir
# run
nextflow run fmalmeida/mpgap -profile singularity [options]
If using conda
You would need to first download the environment file and create the pipeline's conda environment. Example:
Now, everything is set up and ready to run. Remember to always keep your Docker images up to date (Docker pull will always download the latest).