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Bacterial WGS training : Exercise 2

Title Nextflow and Micromamba
Training dataset: None
Questions:
  • How do I load an environment with installed software with micromamba?
  • How do I run a nextflow pipeline?
Objectives:
  • Learn how to use micromamba.
  • Learn how to use nextflow.
Time estimation: 15 min

‼️ Important things to remnenber:

  • Use Tab to automatically complete file names and paths, so it can be easiert to write in the terminal
  • Use keyboard arrows (:arrow_up: :arrow_down:) to move through your terminal's history, so you don't have to write the commands again.
  • Try not to use spaces, accents or special characters like "Ñ" letter, when writting directory of file names.
  • Basic commands you should always remember: pwd cd ls mkdir mv rm rmdir less nano

Go to home, just to be sure everyone is in the same folder

cd
pwd
#Output: /home/alumno
ls

Go to the exercise folder

cd wgs
ls
cd bacterial_wgs_training
ls
#vemos main.nf environment.yml

Micromamba

micromamba is a tiny version of the mamba package manager. micromamba supports a subset of all mamba or conda commands and implements a command line interface from scratch. micromamba is a package manager that enables the installation of any type of software, in this case, bioinformatics software.

The environment.yml allows installing conda environments.

cat environment.yml
# We see all the software that we are going to use in the course
# With micromamba install -f environment.yml, an environment is created with everything we will need for the course
micromamba env list
fastp --help
micromamba activate fastp
#Se carga el ambiente entre parentesis delante del nombre de usuario
fastp --help
micromamba deactivate

How do I use Nextflow?

micromamba activate nextflow
nextflow info
nextflow run main.nf --help

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:

rm results/trace.txt
nextflow run /home/$USER/wgs/bacterial_wgs_training --help

Optionally, we can pass a config file, and specify the .nf script inside a project:

rm results/trace.txt
nextflow -C /home/$USER/wgs/bacterial_wgs_training/nextflow.config \
run /home/$USER/wgs/bacterial_wgs_training/main.nf --help

Finally, let's ask how to use the pipeline:

rm results/trace.txt
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:

rm results/trace.txt
nextflow run BU-ISCIII/bacterial_wgs_training -r one_week_format -profile conda --help