Installation¶

Dependencies¶

This pipeline Nextflow requires Docker, Singularity or conda to run. Please read the information about how to proper choose between conda, docker and singularity profiles.

Installing Nextflow
```
curl -s https://get.nextflow.io | bash
```
Download the pipeline
```
nextflow pull fmalmeida/ngs-preprocess
```

Test your installation

nextflow run fmalmeida/ngs-preprocess --help

Download required tools

# for docker
docker pull fmalmeida/ngs-preprocess:v2.5
nextflow run fmalmeida/ngs-preprocess -profile docker [options]

# for singularity
# remember to properly set NXF_SINGULARITY_LIBRARYDIR
# read more at https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
export NXF_SINGULARITY_LIBRARYDIR=MY_SINGULARITY_IMAGES    # your singularity storage dir
export NXF_SINGULARITY_CACHEDIR=MY_SINGULARITY_CACHE       # your singularity cache dir
singularity pull \
      --dir $NXF_SINGULARITY_LIBRARYDIR \
      fmalmeida-ngs-preprocess-v2.5.img docker://fmalmeida/ngs-preprocess:v2.5
nextflow run fmalmeida/ngs-preprocess -profile singularity [options]

# for conda
wget https://github.com/fmalmeida/ngs-preprocess/raw/master/environment.yml
conda env create -f environment.yml # advice: use mamba
nextflow run fmalmeida/ngs-preprocess -profile conda [options]

(Optional) Install nf-core

pip install nf-core>=1.10

Note

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).