{"id":18964157,"url":"https://github.com/janeliascicomp/nf-demos","last_synced_at":"2026-01-27T02:05:22.223Z","repository":{"id":78049267,"uuid":"355334928","full_name":"JaneliaSciComp/nf-demos","owner":"JaneliaSciComp","description":"Nextflow Demo Pipelines for Image Processing","archived":false,"fork":false,"pushed_at":"2023-12-21T22:46:14.000Z","size":99,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-06-02T07:20:03.556Z","etag":null,"topics":["image-processing","nextflow"],"latest_commit_sha":null,"homepage":"","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/JaneliaSciComp.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-04-06T21:31:07.000Z","updated_at":"2023-05-18T09:35:23.000Z","dependencies_parsed_at":"2025-05-25T22:06:37.455Z","dependency_job_id":"94ab6045-5d01-4ab7-b7b9-08821430d6bd","html_url":"https://github.com/JaneliaSciComp/nf-demos","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/JaneliaSciComp/nf-demos","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-demos","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-demos/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-demos/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-demos/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/nf-demos/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-demos/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28796962,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-27T01:07:07.743Z","status":"online","status_checked_at":"2026-01-27T02:00:07.755Z","response_time":168,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["image-processing","nextflow"],"created_at":"2024-11-08T14:23:05.571Z","updated_at":"2026-01-27T02:05:22.201Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Nextflow demos\n\nThis repository demonstrates a few simple Nextflow pipelines for large data image processing, mainly for working with the n5/zarr image formats. \n\n## Quick Start\n\nThe only software requirements for running this pipeline are [Nextflow](https://www.nextflow.io) (version 20.10.0 or greater) and [Singularity](https://sylabs.io) (version 3.5 or greater). If you are running in an HPC cluster, ask your system administrator to install Singularity on all the cluster nodes.\n\nTo [install Nextflow](https://www.nextflow.io/docs/latest/getstarted.html):\n\n    curl -s https://get.nextflow.io | bash \n\nAlternatively, you can install it as a conda package:\n\n    conda create --name nf-demos -c bioconda nextflow\n\nTo [install Singularity](https://sylabs.io/guides/3.7/admin-guide/installation.html) on CentOS Linux:\n\n    sudo yum install singularity\n\nClone the multifish repository with the following command:\n\n    git clone https://github.com/JaneliaSciComp/nf-demos.git\n\nBefore running the pipeline for the first time, run setup to pull in external dependencies:\n\n    ./setup.sh\n    \nYou can now launch a pipeline, e.g.:\n\n    ./n5-tools-dask/tiff-to-n5.nf.nf [arguments]\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Fnf-demos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjaneliascicomp%2Fnf-demos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Fnf-demos/lists"}