{"id":26149116,"url":"https://github.com/liao961120/minimal-snake","last_synced_at":"2026-04-28T18:01:27.659Z","repository":{"id":117868997,"uuid":"601472350","full_name":"liao961120/minimal-snake","owner":"liao961120","description":"An enhanced template structure for Snakemake","archived":false,"fork":false,"pushed_at":"2023-12-15T08:54:13.000Z","size":432,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-01-26T22:32:18.521Z","etag":null,"topics":["git-bash","make","python","reproducibility","snakemake","snakemake-workflow","windows"],"latest_commit_sha":null,"homepage":"https://yongfu.name/2023/02/15/snakemake/","language":"HTML","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/liao961120.png","metadata":{"files":{"readme":"README.md","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}},"created_at":"2023-02-14T06:12:50.000Z","updated_at":"2023-02-15T03:14:39.000Z","dependencies_parsed_at":"2023-12-31T00:13:15.410Z","dependency_job_id":"dafc4f35-d917-46ca-8c0c-7d875f7bfa6a","html_url":"https://github.com/liao961120/minimal-snake","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/liao961120%2Fminimal-snake","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/liao961120%2Fminimal-snake/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/liao961120%2Fminimal-snake/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/liao961120%2Fminimal-snake/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/liao961120","download_url":"https://codeload.github.com/liao961120/minimal-snake/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242979086,"owners_count":20216120,"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":["git-bash","make","python","reproducibility","snakemake","snakemake-workflow","windows"],"created_at":"2025-03-11T05:28:46.673Z","updated_at":"2026-04-28T18:01:22.618Z","avatar_url":"https://github.com/liao961120.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"A Minimalist Workflow for Snakemake\n===================================\n\nThis workflow structure is modified from Snakemake's [recommended workflow][snk-flow] with two enhancements.\n\n1. **Simplified directory names**\n   \n    `resources/` is renamed as `raw/`, and `results/` is renamed as `made/`. The\n    `workflow/` directory is broken down into `src/` (holding scripts) and the\n    `Snakefile`.\n\n2. **Consistent relative paths**\n   \n    Since `Snakefile` is now placed in the project root, the problem of\n    different relative paths for different directives is resolved, as long as\n    the user always invokes the command `snakemake -c` in the project root.\n\n```tree\n├── README.md\n├── Snakefile\n├── made\n├── raw\n└── src\n```\n\nRefer to [this post][post] for context and details.\n\n\n## Usage\n\n```bash\nbash make.sh    # reproduce everything (e.g., dag.png)\n# snakemake -c  # directly invoke snakemake command\n```\n\n![](dag.png)\n\n\n[snk-flow]: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility\n[post]: https://yongfu.name/2023/02/15/snakemake/\n\n\n---\n\nTo Do\n-----\n\nA simple command line program to take a snakemake's `--detailed-summary` table and generate a dot file of file dependency DAG. This may look like something as:\n\n```bash\nsnakemake --detailed-summary -c | fileDag | dot -Tsvg -Grankdir=LR \u003e dag.svg\n```\n\n```bash\n# snakemake -c\nsnakemake --detatiled-summary -c  # --detailed-summary outputs a TSV file\n```\n\n| output_file              | date                     | rule              | version | log-file(s) | input-file(s)                                                                                              | shellcmd                                                               | status            | plan      |\n| ------------------------ | ------------------------ | ----------------- | ------- | ----------- | ---------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------- | ----------------- | --------- |\n| made/wordfreq.png        | Fri Dec 15 16:26:19 2023 | plot_word_freq    | -       |             | made/merged.csv,made/stopwords.txt,src/viz.R                                                               | Rscript src/viz.R made/merged.csv made/stopwords.txt made/wordfreq.png | ok                | no update |\n| made/CausalModel.csv     | -                        | extract_word_freq | -       |             | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | -                                                                      | removed temp file | no update |\n| made/DeepLearning.csv    | -                        | extract_word_freq | -       |             | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | -                                                                      | removed temp file | no update |\n| made/MultilevelModel.csv | -                        | extract_word_freq | -       |             | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | -                                                                      | removed temp file | no update |\n| made/merged.csv          | Fri Dec 15 16:26:15 2023 | extract_word_freq | -       |             | raw/html/CausalModel.html,raw/html/DeepLearning.html,raw/html/MultilevelModel.html,src/extract_word_freq.R | -                                                                      | ok                | no update |\n| made/stopwords.txt       | Fri Dec 15 16:26:12 2023 | get_stopwords     | -       |             | src/stopwords.R                                                                                            | Rscript src/stopwords.R made/stopwords.txt                             | ok                | no update |\n\n\n### Some Potential Libraries\n\n- [pydot](https://github.com/pydot/pydot)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fliao961120%2Fminimal-snake","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fliao961120%2Fminimal-snake","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fliao961120%2Fminimal-snake/lists"}