https://github.com/SystemsGenetics/KINC-nf
Nextflow pipeline for KINC
https://github.com/SystemsGenetics/KINC-nf
docker nextflow
Last synced: over 1 year ago
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Nextflow pipeline for KINC
- Host: GitHub
- URL: https://github.com/SystemsGenetics/KINC-nf
- Owner: SystemsGenetics
- Created: 2019-01-10T17:25:07.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2022-02-14T21:49:45.000Z (over 4 years ago)
- Last Synced: 2024-10-27T07:32:13.451Z (over 1 year ago)
- Topics: docker, nextflow
- Language: Nextflow
- Size: 3.62 MB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 2
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Metadata Files:
- Readme: README.md
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README
# KINC-nf
The Nextflow pipeline for [KINC](https://github.com/SystemsGenetics/KINC).
## Dependencies
All you need is [nextflow](https://nextflow.io/), [Docker](https://docker.com/), and [nvidia-docker](https://github.com/NVIDIA/nvidia-docker). On HPC systems, you can use [Singularity](https://www.sylabs.io/singularity/) in lieu of Docker. If for some reason you can't use either container software, you will have to install KINC from source.
## Installation
You don't. But you may want to refer to the [config file](https://github.com/SystemsGenetics/KINC-nf/blob/master/nextflow.config) on GitHub file and familiarize yourself with the available settings.
## Usage
You can run the pipeline out-of-the-box with Nextflow. We also provide some example data to get you started. Here's how to run KINC on the example data:
```bash
nextflow run systemsgenetics/kinc-nf -profile example,
```
This example will download the pipeline repository, the example data, and the Docker/Singularity container for KINC, and run KINC on the example data. The results will be saved to `./output`.
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 specify any of the params in `nextflow.config` as command-line arguments, for example:
```bash
nextflow run systemsgenetics/kinc-nf \
--similarity_chunks 1 \
--similarity_hardware_type gpu
```
The params allow you to control which analytics to run, how many chunks to use where applicable, and various other command-line parameters for KINC. You can resume a failed run with the `-resume` flag. Consult the Nextflow documentation for more information on these and other options.
## Palmetto
To run KINC-nf on Palmetto, you have to use Singularity instead of Docker, and use the `palmetto` profile:
```bash
nextflow run systemsgenetics/kinc-nf -profile palmetto,singularity
```
## Kubernetes
You can run this pipeline, as well as any other nextflow pipeline, on a [Kubernetes](https://kubernetes.io/) cluster with minimal effort. Consult the [kube-runner](https://github.com/SystemsGenetics/kube-runner) repo for instructions.