Downloading the pipeline
You can easily get a copy of the pipeline with:
Downloading docker images
The pipeline uses both custom and public images. All images can be downloaded on the fly, automatically by nextflow, and this is the recommended way to do it.
The images are defined like the following:
And could be downloaded like this:
You would need to do it for each image.
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, to download the images for docker you may:
Bacannot databases are not inside the docker images anymore to avoid huge images and problems with connections and limit rates with dockerhub.
Users can directly download pre-formatted databases from Zenodo: https://doi.org/10.5281/zenodo.7615811
Useful for standardization and also overcoming known issues that may arise when formatting databases with
A module to download the latest pre-formatted database has also been made available:
I want to generate a new formatted database
Testing your installation
After that, you can run the pipeline with a testing dataset by selecting one of the available profiles:
nextflow run fmalmeida/mpgap -profile docker,test--bacannot_db ./bacannot_dbs
nextflow run fmalmeida/mpgap -profile singularity,test--bacannot_db ./bacannot_dbs
About NF profiles
Please read more about how to proper select NF profiles to better understand it.