Nextflow Pipelines

Table of Contents

• Nextflow Pipelines
  • Table of Contents
  • Background
  • Accessing old pipelines/versions
  • Installation
    • Clone the pipeline repository
    • Test the installation
  • External software dependencies
  • Wiki
  • Citation
  • Author information

Background

This repository is a collection of Nextflow workflows that I've written relating to projects I've worked on. This repository acts as the implicit workflow, calling sub-workflows which are stored in the git submodule nf-workflows. The sub-workflows use 'processes' stored in the nf-modules git submodule.

The idea is to have workflows that generally follow best-practices with code that is publication ready.

Accessing old pipelines/versions

I've made some significant changes to how my pipelines operate recently. At the time of writing, the master branch of this repository only has a few of the sub-workflows I've implemented.

To access the old version of this pipeline, download this version (2f89cd6).

Installation

Before doing anything, ensure you have a working installation of Nextflow on your system. Visit the installation page for details on how to do that.

The pipeline also utilises Conda for software management. This can be installed following the instructions provided here.

Clone the pipeline repository

Clone this repository using the following command

git clone --recurse-submodules https://github.com/a-lud/nf-pipelines.git

NOTE: It's important to install the software to a location that has a reasonable amount of storage space. The pipeline will create a 'conda cache' directory inside this repository which houses all the environments used by this pipeline.

Test the installation

To check that Nextflow and the pipeline 'works', try calling the help page

nextflow run /path/to/nf-pipelines/main.nf --help

The pipelines help page can be called using the '--help' command. Help pages for specific sub-workflows can be called by passing the sub-workflow name to the help command.

nextflow run /path/to/nf-pipelines/main.nf --help assembly

If you encounter any errors, come back here and I'll try and help out.

External software dependencies

I've attempted to use conda where I can for software dependencies. Unfortunately I've not been able to package everything. Ensure the following softare are installed manually:

• pin_hic - A lightweight scaffolding tool that produces results similar to SALSA2 (GitHub)
• satool - used to convert the SAT file produced by pin_hic to AGP format (GitHub)

I also note here that many of the scripts in the bin directory are not my own and all credit goes to the authors. I've simply aggregated the scripts I need in this repository. I've tried to make it clear in the scripts where I've got them if the information is not already present.

Wiki

I've written a lot of documentation in the wiki, which can be accessed from tab at the top of the page, or from this link.

I highly recommend at least reading the Getting Started entry to become familiar with the pipeline (especially the storage requirements!).

Citation

If you use any of the pipelines within this repository, please link to this repo and that'll be more than enough.

Author information

Alastair Ludington
alastair.ludington@adelaide.edu.au
PhD Candidate, The University of Adelaide