{"id":13429375,"url":"https://github.com/SystemsGenetics/KINC-nf","last_synced_at":"2025-03-16T03:31:22.379Z","repository":{"id":44610947,"uuid":"165101889","full_name":"SystemsGenetics/KINC-nf","owner":"SystemsGenetics","description":"Nextflow pipeline for KINC","archived":false,"fork":false,"pushed_at":"2022-02-14T21:49:45.000Z","size":3797,"stargazers_count":1,"open_issues_count":2,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-10-27T07:32:13.451Z","etag":null,"topics":["docker","nextflow"],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SystemsGenetics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-01-10T17:25:07.000Z","updated_at":"2021-10-19T21:35:53.000Z","dependencies_parsed_at":"2022-09-25T00:34:42.615Z","dependency_job_id":null,"html_url":"https://github.com/SystemsGenetics/KINC-nf","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SystemsGenetics%2FKINC-nf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SystemsGenetics%2FKINC-nf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SystemsGenetics%2FKINC-nf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SystemsGenetics%2FKINC-nf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SystemsGenetics","download_url":"https://codeload.github.com/SystemsGenetics/KINC-nf/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243822312,"owners_count":20353496,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["docker","nextflow"],"created_at":"2024-07-31T02:00:36.139Z","updated_at":"2025-03-16T03:31:21.956Z","avatar_url":"https://github.com/SystemsGenetics.png","language":"Nextflow","funding_links":[],"categories":["GitHub Repositories"],"sub_categories":[],"readme":"# KINC-nf\n\nThe Nextflow pipeline for [KINC](https://github.com/SystemsGenetics/KINC).\n\n## Dependencies\n\nAll 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.\n\n## Installation\n\nYou 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.\n\n## Usage\n\nYou 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:\n```bash\nnextflow run systemsgenetics/kinc-nf -profile example,\u003cdocker|singularity\u003e\n```\n\nThis 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`.\n\nKINC-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.\n\nYou can specify any of the params in `nextflow.config` as command-line arguments, for example:\n```bash\nnextflow run systemsgenetics/kinc-nf \\\n    --similarity_chunks 1 \\\n    --similarity_hardware_type gpu\n```\n\nThe 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.\n\n## Palmetto\n\nTo run KINC-nf on Palmetto, you have to use Singularity instead of Docker, and use the `palmetto` profile:\n```bash\nnextflow run systemsgenetics/kinc-nf -profile palmetto,singularity\n```\n\n## Kubernetes\n\nYou 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSystemsGenetics%2FKINC-nf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FSystemsGenetics%2FKINC-nf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSystemsGenetics%2FKINC-nf/lists"}