Running pipelines

By default, we run nf-core pipelines. To run a pipeline, read the official documentation with an example.

Monitoring runs with Nextflow Tower

This is a guide on how to use Nextflow Tower to monitor nf-core pipeline runs.

We have created an API token for our GitHub account (brickmanlab) and restricted it to run only pipelines, nothing else. The TOWER_WORKSPACE_ID and TOWER_ACCESS_TOKEN are stored in Brickman/config/brickman.bashrc.

To do more advance stuff, you have to create your own personal access token.

Tower CLI installation

The tower cli¹ is required to be installed only once to connect the server as a computing resource. Afterward, it's not required any more².

# Download the latest version of Tower CLI:
wget https://github.com/seqeralabs/tower-cli/releases/download/v0.7.3/tw-0.7.3-linux-x86_64

# Make the file executable and move to directory accessible by $PATH variable:
mkdir ~/.local/bin && mv tw-* tw && chmod +x ~/.local/bin/tw