08_containers.qmd

---
title: "Containers"
engine: knitr
---


## Overview

Containers such as Docker and apptainer address two issues:

- making pipeline reproducible,
- we do not have root access in HPC. 


## Using an existing container

In the file `nextflow.config` provided in `nf-nest` we 
provide an example of container configuration:

```{bash}
head -n 28 experiment_repo/nextflow.config
```

There are two profiles, the `default` one using Docker, and the 
`cluster` one, using `apptainer`. We define a label for this 
container, which we call here `containerized`. 

To instruct one of the process in the workflow to use that 
container, add the directive `label 'containerized'`. 

Here is an example of a process to compile and run a [Stan program](https://mc-stan.org/), 
where Stan is part of the above container:

```{groovy}
#| eval: false
#| file: experiment_repo/nf-nest/examples/stan.nf
```

Here is an example workflow using these containerized processes:

```{groovy}
#| eval: false
#| file: experiment_repo/nf-nest/examples/stan_example.nf
```

To run it:

```{bash}
cd experiment_repo
./nextflow run nf-nest/examples/stan_example.nf -profile cluster
```


## Creating containers

There are many reference online for creating containers in general, but much less on 
creating cross-platform containers working on both x86 and Apple Silicon. 

We have created some script to help doing this, see [code and instructions at this page](https://github.com/UBC-Stat-ML/containers).