{"id":18448829,"url":"https://github.com/sequana/sequana_pipeline_template","last_synced_at":"2026-02-11T16:36:06.893Z","repository":{"id":48531510,"uuid":"223495124","full_name":"sequana/sequana_pipeline_template","owner":"sequana","description":"a cookiecutter sequana pipeline template","archived":false,"fork":false,"pushed_at":"2024-08-08T08:15:56.000Z","size":91,"stargazers_count":0,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-02-18T00:51:26.809Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sequana.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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}},"created_at":"2019-11-22T22:13:35.000Z","updated_at":"2024-08-08T08:15:59.000Z","dependencies_parsed_at":"2024-08-08T09:25:53.264Z","dependency_job_id":null,"html_url":"https://github.com/sequana/sequana_pipeline_template","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_pipeline_template","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_pipeline_template/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_pipeline_template/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fsequana_pipeline_template/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/sequana_pipeline_template/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247760628,"owners_count":20991517,"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":"2024-11-06T07:17:24.611Z","updated_at":"2026-02-11T16:36:01.871Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"=========================\nSequana Pipeline Template\n=========================\n\n:version: 2.0\n\nThis repository is a Cookiecutter template to start a new `Sequana pipeline \u003chttps://sequana.readthedocs.io\u003e`_ \nimplementation from scratch.\n\n\nQuickstart\n----------\n\nYou first need to install the latest version of **cookiecutter** if you haven't installed it yet (requires\nCookiecutter 1.4.0 or higher)::\n\n    pip install -U cookiecutter\n\nThen, no need to install the sequana_pipeline_template package itself. You can call it directly from github as\nfollows::\n\n    cookiecutter https://github.com/sequana/sequana_pipeline_template.git\n\nyou will be asked some questions in particular the name of the package. You can\nchange things later on. Except the name, most entries are populated in the\nsetup.py file.\n\n- The first question asks the name of the future pipeline. There is no strict\nconvention in Sequana but we usually use small caps and underscores to separate\nwords (e.g., sequana_rnaseq).\n\n- The second question is the short description that will be added to your\nsetup.py configuration file\n\n- The third questions asked for keywords, also added to the setup.py\n\nThat's it.\n\n\nIf your pipeline is called **varseq**, you should end up with a structure in the\ndirectory **sequana_varseq** similar to ::\n\n\nsimilar to ::\n\n    ├── test\n    │   └── __init__.py\n    ├── doc\n    │   ├── conf.py\n    │   ├── index.rst\n    │   └── Makefile\n    ├── README.rst\n    ├── requirements.txt\n    ├── sequana_pipelines\n    │   └── varseq\n    │       ├── config.yaml\n    │       ├── __init__.py\n    │       ├── main.py\n    │       ├── varseq.rules\n    │       ├── README.rst\n    │       ├── requirements.txt\n    │       └── schema.yaml\n    │       └── data\n    │           ├── __init__.py\n    ├── setup.cfg\n    └── setup.py\n\nYou can install this new pipeline as follows::\n\n    cd sequana_varseq\n    python setup.py install\n\nYou can build the documentation as follows::\n\n    cd sequana_varseq/doc\n    make html  # under linux\n\nOr test it::\n\n    cd sequana_varseq\n    pytest  # this tool (pytest) must be install first (pip install pytest)\n\nOf course, you now need to work a little bit by replacing the content of some\nfiles with your code and/or documentation and tests.\n\nThe most important editing steps are then:\n\n1. to edit the *config.yaml* and *varseq.rules* in the sequana_pipelines/varseq\n   directory with your own snakemake pipeline and configuration file.\n2. edit the main script **main.py** and adapt it to your needs. This will be the\n   entry point of the user.\n3. the documentation in ./doc\n4. test in ./test\n5. update the requirements.txt file in varseq/ directory to add any external\n   dependencies. The requirements.txt at the top level is only for Python\n   dependencies. In principle it depends only on sequana\n\nOnce done, create a repository on https://github.com/sequana/sequana_varseq and\nupload your files. \n\nThis is not perfect and we will most probably edit this template in the future\nto make it more robust and possibly add such features (help needed).\n\nOnce happy, you can create a local repository::\n\n    git init\n\nCreate and switch to main branch: if you are on a different branch, \nyou can create and switch to the main branch with::\n\n    git checkout -b main\n\nAdd and commit changes: ensure you have at least one commit in your\nrepository. Make an initial commit::\n\n    git add .\n    git commit -m \"Initial commit\"\n\nPush to Remote Repository: try pushing to the remote repository::\n\n    git remote add origin git@github.com:sequana/your_repo\n    git push -u origin main\n\n\nChangelog\n\n* v2: uses poetry\n* v1: uses setuptools\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fsequana_pipeline_template","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fsequana_pipeline_template","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fsequana_pipeline_template/lists"}