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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:

# nextflow pull
nextflow pull fmalmeida/ngs-preprocess

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 you want to download it yourself, you can do it like the following:

docker pull fmalmeida/ngs-preprocess:v2.6

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:

# apply this command to each image
# just change the "/" and ":" for "-".
# E.g. Image fmalmeida/ngs-preprocess:v2.6 becomes fmalmeida-ngs-preprocess-v2.6.img
singularity pull \
    --dir $NXF_SINGULARITY_LIBRARYDIR \
    fmalmeida-ngs-preprocess-v2.6.img docker://fmalmeida/ngs-preprocess:v2.6

If using conda

You would need to first download the environment file and create the pipeline's conda environment. Example:

wget https://github.com/fmalmeida/ngs-preprocess/raw/master/environment.yml
conda env create -f environment.yml # advice: use mamba

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).