The Nextflow pipeline for KINC.

All you need is nextflow, Docker, and nvidia-docker. On HPC systems, you can use Singularity in lieu of Docker. If for some reason you can't use either container software, you will have to install KINC from source.

You don't. But you may want to copy the nextflow.config file from this repo so that you can customize it:

wget https://raw.githubusercontent.com/SystemsGenetics/KINC-nf/master/nextflow.config

Use nextflow to run this pipeline. For example, here is a basic usage:

nextflow run systemsgenetics/KINC-nf

This example will download this pipeline to your machine and use the default nextflow.config in this repo. It will assume that you have KINC installed natively, and it will process all GEM files in the input directory, saving all output files to the output directory, as defined in nextflow.config.

KINC-nf detects input files by their file extension. For example, the default extension for GEM files is *.emx.txt, so make sure that your input GEMs have this extension before running the pipeline. You can also place intermediate files in the input directory, and KINC-nf will use them as inputs to the appropriate processes. For example, you can provide the *.emx file created by import_emx instead of the plain-text GEM and KINC-nf will skip the import_emx step.

You can also create your own nextflow.config file; nextflow will check for a config file in your current directory before defaulting to config file in this repo. You will most likely need to customize this config file as it provides options such as which analytics to run, how many chunks to use where applicable, and various other command-line parameters for KINC. The config file also allows you to define your own "profiles" for running this pipeline in different environments. Consult the Nextflow documentation for more information on what environments are supported.

To use Docker or Singularity, run nextflow with the -with-docker or -with-singularity flag. You can resume a failed run with the -resume flag. Consult the Nextflow documentation for more information on these and other options.

To run KINC-nf on Palmetto, you have to use Singularity instead of Docker. First, add the singularity module:

# also append this command to your .bashrc
module add singularity

Then whenever you run nextflow, you must tell it to use the PBS profile and Singularity:

nextflow run systemsgenetics/KINC-nf -profile pbs -with-singularity

You can run this pipeline, as well as any other nextflow pipeline, on a Kubernetes cluster with minimal effort. Consult the kube-runner repo for instructions.