Main repository for Olm lab bioinformatics pipelines.
Author: Parsa Ghadermazi (pagh1940@colorado.edu)
This repository contains Nextflow pipelines for computational research in the Olm lab at University of Colorado Boulder. The pipelines are designed to be modular and reusable, allowing for easy integration into various bioinformatics workflows.
There are currently two ways to run this code- one of which is based on roadmaps, and one of which is based on entry points. They have different documentation, as outlined below.
Documentation for roadmap-based workflows
Documentation for entry-based workflows
Basic testing is provided using the nf-test framework. Before running the tests, find the best execution environment profile for the test. Currently, there are three main profiles available: apptainer, docker, local. The rest of the profiles are cluster-specific settings. Use apptainer or docker if you have either of these container tools installed. If you want to run without a container choose local. Note that when using local you have to have all the required tools in each workflow installed. Once you figure out the environment, run the following command from the base directory of this repo to run all tests:
$ nf-test test --profile <docker|apptainer|local,other_profiles>
As an example, the right way to test the pipelines on alpine HPC is:
$ nf-test test --profile apptainer,alpine