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.
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).
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 this repository using the following command
git clone --recurse-submodules https://github.com/a-lud/nf-pipelines.gitNOTE: 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.
To check that Nextflow and the pipeline 'works', try calling the help page
nextflow run /path/to/nf-pipelines/main.nf --helpThe 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 assemblyIf you encounter any errors, come back here and I'll try and help out.
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 bypin_hicto 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.
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!).
If you use any of the pipelines within this repository, please link to this repo and that'll be more than enough.
Alastair Ludington
alastair.ludington@adelaide.edu.au
PhD Candidate, The University of Adelaide