Скачать или смотреть Hello Nextflow - Part 5: Hello Containers

In Parts 1-4 of this training course, you learned how to use the basic building blocks of Nextflow to assemble a simple workflow capable of processing some text, parallelizing execution if there were multiple inputs, and collecting the results for further processing.

However, you were limited to basic UNIX tools available in your environment. Real-world tasks often require various tools and packages not included by default. Typically, you'd need to install these tools, manage their dependencies, and resolve any conflicts.

That is all very tedious and annoying, so we're going to show you how to use containers to solve this problem much more conveniently.

A container is a lightweight, standalone, executable unit of software created from a container image that includes everything needed to run an application including code, system libraries and settings.

https://training.nextflow.io/2.1.1/he...

00:00 Welcome
01:25 0. Warmup: Run hello-containers.nf
01:36 1. Use a container 'manually'
03:04 1.1. Pull the container image
04:47 Pulling a Singularity image
05:46 1.2. Use the container to run cowpy as a one-off command
06:27 1.3. Use the container to run cowpy interactively
07:37 1.3.2. Run the desired tool command(s)
08:09 1.3.3. Exit the container
08:26 1.3.4. Mount data into the container
09:06 1.3.5. Use the mounted data
09:55 2. Use containers in Nextflow
10:06 2.1. Write a cowpy module
11:01 2.2. Add cowpy to the workflow
11:49 2.2.4. Run the workflow to verify that it works
12:28 2.3. Use a container to run it
13:07 2.3.2. Enable use of Docker via the nextflow.config file
13:32 2.3.3. Run the workflow with Docker enabled
13:58 2.3.4. Inspect how Nextflow launched the containerized task