cd
pwd
#Output: /home/alumno
ls
cd wgs
ls
cd bacterial_wgs_training
ls
#vemos main.nf environment.yml
El yml permite instalar environments de conda.
Conda es un gestor de paquetes para poder instalar software de cualquier tipo, en este caso de bioinfo.
cat environment.yml
#Vemos todo el software que vamos a usar en el curso
#Con el conda install -f environment.yml se nos crea un environment con todo lo que vamos a necesitar para el curso
conda env list
fastp --help
conda activate fastp
#Se carga el ambiente entre parentesis delante del nombre de usuario
fastp --help
conda deactivate
conda activate nextflow
nextflow info
nextflow run main.nf --help
Ejemplo desde github:
nextflow run BU-ISCIII/bacterial_wgs_training -r one_week_format --help
#Ejemplo de un pipeline de nfcore con versiones y eso
So, what now? In order to execute a nextflow pipeline, we need to tell it to run a project which contains a main.nf script written in groovy + the pipeline languages:
nextflow run /home/$USER/wgs/bacterial_wgs_training --help
Optionally, we can pass a config file, and specify the .nf script inside a project:
nextflow -C /home/$USER/wgs/bacterial_wgs_training/nextflow_2.config \
run /home/$USER/wgs/bacterial_wgs_training/main.nf --help
Finally, let's ask how to use the pipeline:
nextflow run BU-ISCIII/bacterial_wgs_training -r one_week_format --help
There is one big detail left. The software needed to execute the pipeline is no installed in our machine. Thankfully, we have a conda environment ready for this course, and our pipeline has already being configurated to know where to find it and how to use it. Use the right argument and go for it:
nextflow run BU-ISCIII/bacterial_wgs_training -r one_week_format -profile conda --help