Creating a Pipeline from Scratch

Introduction

This tutorial shows you how to start a new pipeline from scratch

• prepare linux tool + validation inputs

• wrap in Nextflow

• wrap the pipeline in Bench

Start Bench workspace

• For this tutorial, any instance size will work, even the smallest standard-small.

• Select the single user workspace permissions (aka "Access limited to workspace owner "), which allows us to deploy pipelines.

• A small amount of disk space (10GB) will be enough.

We are going to wrap the "gzip" linux compression tool with inputs:

• 1 file

• compression level: integer between 1 and 9

Here is an example of NextFlow code that wraps the bzip2 command and publishes the final output in the “out” folder:

Save this file as nextflow-src/main.nf, and check that it works:

We now need to:

• Use Docker

• Follow some nf-core best practices to make our source+test compatible with the pipeline-dev tools

In NextFlow, Docker images can be specified at the process level

• Each process may use a different docker image

• It is highly recommended to always specify an image. If no Docker image is specified, Nextflow will report this. In ICA, a basic image will be used but with no guarantee that the necessary tools are available.

Specifying the Docker image is done with the container '<image_name:version>' directive, which can be specified

• at the start of each process definition

• or in nextflow config files (preferred when following nf-core guidelines)

For example, create nextflow-src/nextflow.config:

We can now run with nextflow's -with-docker option:

Following some nf-core to make our source+test compatible with the pipeline-dev tools:

Here is an example of “test” profile that can be added to nextflow-src/nextflow.config to define some input values appropriate for a validation run:

With this profile defined, we can now run the same test as before with this command:

A “docker” profile is also present in all nf-core pipelines. Our pipeline-dev tools will make use of it, so let’s define it:

We can now run the same test as before with this command:

We also have enough structure in place to start using the pipeline-dev command:

In order to deploy our pipeline to ICA, we need to generate the user interface input form.

This is done by using nf-core's recommended nextflow_schema.json.

For our simple example, we generate a minimal one by hand (done by using one of the nf-core pipelines as example):

In the next step, this gets converted to the ica-flow-config/inputForm.json file.

We just need to create a final file, which we had skipped until now: Our project description file, which can be created via the command pipeline-dev project-info --init:

We can now run:

After generating the ICA-Flow-specific files in the ica-flow-config folder (JSON input specs for Flow launch UI + list of inputs for next step's validation launch), the tool identifies which previous versions of the same pipeline have already been deployed (in ICA Flow, pipeline versioning is done by including the version number in the pipeline name).

It then asks if we want to update the latest version or create a new one.

Choose "3" and enter a name of your choice to avoid conflicts with all the others users following this same tutorial.

At the end, the URL of the pipeline is displayed. If you are using a terminal that supports it, Ctrl+click or middle-click can open this URL in your browser.

This launches an analysis in ICA Flow, using the same inputs as the pipeline's "test" profile.

Some of the input files will have been copied to your ICA project in order for the analysis launch to work. They are stored in the folder /data/project/bench-pipeline-dev/temp-data.