{"id":22188412,"url":"https://github.com/vmikk/phylotwin-preprocessor","last_synced_at":"2025-03-24T20:14:40.720Z","repository":{"id":258612412,"uuid":"865829734","full_name":"vmikk/phylotwin-preprocessor","owner":"vmikk","description":"Species occurrence pre-processing pipeline","archived":false,"fork":false,"pushed_at":"2025-02-12T09:30:57.000Z","size":718,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-12T10:33:40.026Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vmikk.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-10-01T07:53:13.000Z","updated_at":"2025-02-12T09:31:01.000Z","dependencies_parsed_at":"2025-01-09T13:20:47.832Z","dependency_job_id":"c993f0f2-1333-4060-ba38-59eeb9ddbf71","html_url":"https://github.com/vmikk/phylotwin-preprocessor","commit_stats":null,"previous_names":["vmikk/phylotwin-preprocessor"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2Fphylotwin-preprocessor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2Fphylotwin-preprocessor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2Fphylotwin-preprocessor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vmikk%2Fphylotwin-preprocessor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vmikk","download_url":"https://codeload.github.com/vmikk/phylotwin-preprocessor/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245344005,"owners_count":20599867,"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":[],"created_at":"2024-12-02T11:10:23.186Z","updated_at":"2025-03-24T20:14:40.686Z","avatar_url":"https://github.com/vmikk.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PhyloTwin-Preprocessor - GBIF Occurrence Data Processing Pipeline\n\nA Nextflow pipeline for processing GBIF species occurrence data with spatial outlier detection and H3 grid binning. \n\nThe pipeline offers two processing modes:\n- \"Atomic\" mode: Processes each species independently\n- \"Batched\" mode: Processes multiple species in batches (optimized for HPC environments)\n\n\n# Dependencies\n\n## Primary dependencies\n\nThese are the tools that the user must install and configure on their system to run the pipeline:\n\n- [Nextflow](https://www.nextflow.io/) \u003e= 24.10 (requires [Java](https://www.java.com/en/) \u003e= 17 \u0026 \u003c= 23)\n- [Singularity](https://sylabs.io/)/[Apptainer](https://apptainer.org/) or [Docker](https://www.docker.com/)\n\n## Secondary dependencies\n\nThese are the containerized tools or packages required by the pipeline, which will be automatically handled within the containers:\n\n- [DuckDB](https://duckdb.org/)\n- [ELKI](https://elki-project.github.io/)\n- [R](https://www.r-project.org/)\n- [Python](https://www.python.org/)\n- [GNU Parallel](https://www.gnu.org/software/parallel/)\n- [aria2](https://aria2.github.io/)\n- [jq](https://github.com/jqlang/jq)\n\nR packages:\n- [data.table](https://rdatatable.gitlab.io/data.table/)\n- [ape](https://github.com/emmanuelparadis/ape)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvmikk%2Fphylotwin-preprocessor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvmikk%2Fphylotwin-preprocessor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvmikk%2Fphylotwin-preprocessor/lists"}