Installation
Dependencies
The pipeline require only a UNIX system, Nextflow and either Docker or Singularity. Please, for installing these tools refer to their manual.
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
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.
If you want to download it yourself, you can find all the images used in the pipeline described in the file docker.config (for docker) and singularity.config (for singularity).
The images are defined like the following:
...
withLabel: 'db_download|db_tools|misc' {
container = 'fmalmeida/bacannot@sha256:0648797837cd8e11b6abd40745cafc0db81647953921ec54ce0ceef9ecef6450'
}
...
And could be downloaded like this:
docker pull fmalmeida/bacannot@sha256:0648797837cd8e11b6abd40745cafc0db81647953921ec54ce0ceef9ecef6450
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
Bacannot databases are not inside the docker images anymore to avoid huge images and problems with connections and limit rates with dockerhub.
Pre-formatted
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 singularity profile.
A module to download the latest pre-formatted database has also been made available:
# Download pipeline pre-built databases
nextflow run fmalmeida/bacannot \
--get_zenodo_db \
--output ./ \
-profile <docker/singularity>
I want to generate a new formatted database
# Download pipeline databases
nextflow run fmalmeida/bacannot \
--get_dbs \
--output bacannot_dbs \
-profile <docker/singularity>
Testing your installation
After that, you can run the pipeline with a testing dataset by selecting one of the available profiles:
- Docker
nextflow run fmalmeida/mpgap -profile docker,test--bacannot_db ./bacannot_dbs
- Singularity
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.