8 | {%- else %} 9 |

10 | {%- endif %} 11 | {%- block body %}{%- endblock %} 12 |

13 | {%- endblock main %} 14 | -------------------------------------------------------------------------------- /source/_templates/workflow_page.md: -------------------------------------------------------------------------------- 1 | 2 | # {{ wf["full_name"] }} 3 | 4 | ::::{grid} 4 5 | {% for badge in ["license", "issues", "stars", "watchers"] %} 6 | :::{grid-item} 7 | :columns: auto 8 | :margin: 0 9 | :padding: 1 10 | ![](https://img.shields.io/github/{{ badge }}/{{ wf["full_name"] }}?style=flat&label={{ badge }}) 11 | ::: 12 | {% endfor %} 13 | :::{grid-item} 14 | :columns: auto 15 | :margin: 0 16 | :padding: 1 17 | [![](https://img.shields.io/badge/GitHub%20page-blue?style=flat)](https://github.com/{{ wf["full_name"] }}) 18 | ::: 19 | :::: 20 | 21 | {{ wf["description"] }} 22 | 23 | ## Overview 24 | 25 | **Topics:** {% for t in wf["topics"] %} {bdg-secondary}`{{ t }}` {% endfor %} 26 | 27 | 28 | **Latest release:** {bdg-primary}`{{ wf["release"] }}`, **Last update:** {bdg-primary}`{{ wf["last_update"] }}` 29 | 30 | 31 | **Linting:** 32 | {% if wf["linting"] == None -%} 33 | {bdg-success}`linting: passed` 34 | {%- else -%} 35 | {bdg-ref-danger}`linting: failed ` 36 | {%- endif -%}, 37 | **Formatting:** 38 | {% if wf["formatting"] == None -%} 39 | {bdg-success}`formatting: passed` 40 | {%- else -%} 41 | {bdg-ref-danger}`formatting: failed ` 42 | {%- endif %} 43 | 44 | ## Deployment 45 | 46 | ### Step 1: Install Snakemake and Snakedeploy 47 | 48 | Snakemake and Snakedeploy are best installed via the [Mamba package manager](https://github.com/mamba-org/mamba) (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install [Miniforge](https://github.com/conda-forge/miniforge). 49 | More details regarding Mamba can be found [here](https://github.com/mamba-org/mamba). 50 | 51 | When using Mamba, run 52 | 53 | ```bash 54 | mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy 55 | ``` 56 | 57 | to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated _via_ 58 | 59 | ```bash 60 | conda activate snakemake 61 | ``` 62 | 63 | ### Step 2: Deploy workflow 64 | 65 | With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. 66 | First, create an appropriate project working directory on your system and enter it: 67 | 68 | ```bash 69 | mkdir -p path/to/project-workdir 70 | cd path/to/project-workdir 71 | ``` 72 | 73 | In all following steps, we will assume that you are inside of that directory. Then run 74 | 75 | ```bash 76 | snakedeploy deploy-workflow https://github.com/{{ wf["full_name"] }} . --tag {{ wf["release"] }} 77 | ``` 78 | 79 | Snakedeploy will create two folders, `workflow` and `config`. The former contains the deployment of the chosen workflow as a [Snakemake module](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-and-combining-pre-exising-workflows), the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs. 80 | 81 | ### Step 3: Configure workflow 82 | 83 | To configure the workflow, adapt `config/config.yml` to your needs following the [instructions below](#configuration). 84 | 85 | ### Step 4: Run workflow 86 | 87 | The deployment method is controlled using the `--software-deployment-method` (short `--sdm`) argument. 88 | 89 | {% for depl in wf.deployment %} 90 | {%- if depl == 'conda' %} 91 | 92 | To run the workflow with automatic deployment of all required software via `conda`/`mamba`, use 93 | 94 | ```bash 95 | snakemake --cores all --sdm conda 96 | ``` 97 | 98 | {%- endif -%} 99 | {%- if depl == 'apptainer' %} 100 | 101 | To run the workflow using `apptainer`/`singularity`, use 102 | 103 | ```bash 104 | snakemake --cores all --sdm apptainer 105 | ``` 106 | 107 | {%- endif -%} 108 | {%- if depl == 'apptainer+conda' %} 109 | 110 | To run the workflow using a combination of `conda` and `apptainer`/`singularity` for software deployment, use 111 | 112 | ```bash 113 | snakemake --cores all --sdm conda apptainer 114 | ``` 115 | 116 | {%- endif -%} 117 | {% endfor %} 118 | 119 | Snakemake will automatically detect the main `Snakefile` in the `workflow` subfolder and execute the workflow module that has been defined by the deployment in [step 2](#step-2-deploy-workflow). 120 | 121 | For further options such as cluster and cloud execution, see [the docs](https://snakemake.readthedocs.io/). 122 | 123 | ### Step 5: Generate report 124 | 125 | After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using 126 | 127 | ```bash 128 | snakemake --report report.zip 129 | ``` 130 | 131 | ## Configuration 132 | 133 | _The following section is imported from the workflow's `config/README.md`_. 134 | 135 | {{ wf["config_from_readme"] }} 136 | 137 | ## Linting and formatting 138 | 139 | (linting-{{ wf["full_name"]|slugify }})= 140 | ### Linting results 141 | 142 | {% if wf["linting"] == None %} 143 | ``` 144 | All tests passed! 145 | ``` 146 | {%- else -%} 147 | 148 |

149 | 150 | ```{code-block} 151 | :linenos: 152 | 153 | {{ wf["linting"] }} 154 | ``` 155 |

156 | 157 | {% endif %} 158 | 159 | (formatting-{{ wf["full_name"]|slugify }})= 160 | ### Formatting results 161 | 162 | {% if wf["formatting"] == None %} 163 | ``` 164 | All tests passed! 165 | ``` 166 | {%- else -%} 167 | 168 |

169 | 170 | ```{code-block} 171 | :linenos: 172 | 173 | {{ wf["formatting"] }} 174 | ``` 175 |

176 | 177 | {% endif %} 178 | -------------------------------------------------------------------------------- /source/_templates/workflows_by.md: -------------------------------------------------------------------------------- 1 | # Top workflows by {{ input[0]["metric"] }} 2 | 3 | ::::{grid} 3 4 | 5 | {% for repo in input -%} 6 | 7 | :::{grid-item-card} [{{ repo["name"] }}]() 8 | 9 | {{ repo["user"] }} 10 | 11 | ^^^ 12 | 13 | {{ repo["description"] }} 14 | 15 | --- 16 | 17 | {bdg-muted}`Updated: {{ repo["last_update"] }}` 18 | {bdg-muted}`Release: {{ repo["latest_release"] }}` 19 | {%- for qc in ["formatting", "linting"] -%} 20 | {%- if repo[qc] == None -%} 21 | {bdg-success}`{{qc}}: passed` 22 | {%- else -%} 23 | {bdg-danger}`{{qc}}: failed` 24 | {%- endif -%} 25 | {% endfor %} 26 | 27 | +++ 28 | 29 | {octicon}`feed-star;1.0em;sd-text-success` 30 | {bdg-primary-line}`{{ repo["stargazers_count"] }} stars` 31 | 32 | {octicon}`eye;1.0em;sd-text-success` 33 | {bdg-primary-line}`{{ repo["subscribers_count"] }} watchers` 34 | ::: 35 | {% endfor %} 36 | 37 | :::: 38 | 39 | ```{toctree} 40 | :hidden: 41 | 42 | {% for repo in input -%} 43 | workflows/{{ repo["full_name"] }} 44 | {% endfor %} 45 | ``` 46 | -------------------------------------------------------------------------------- /source/build_wf_pages.py: -------------------------------------------------------------------------------- 1 | import json 2 | import re 3 | from jinja2 import Environment, FileSystemLoader, select_autoescape 4 | from datetime import datetime 5 | from pathlib import Path 6 | 7 | 8 | def check_readme(readme): 9 | clean_readme = [] 10 | readme_split = readme.split("\n") 11 | code_block = False 12 | for i, j in zip(readme_split, range(0, len(readme_split))): 13 | if i.startswith("```"): 14 | code_block = not code_block 15 | if i.startswith("# ") and not code_block: 16 | clean_readme += [i.replace("# ", "## ")] 17 | else: 18 | clean_readme += [i] 19 | return "\n".join(clean_readme) 20 | 21 | 22 | def check_deployment(depl): 23 | result = {} 24 | for i in depl.keys(): 25 | if depl[i]: 26 | result[i.replace("singularity", "apptainer")] = True 27 | return result 28 | 29 | 30 | def check_qc_output(qc_item, max_lines=200): 31 | if qc_item is None: 32 | return None 33 | else: 34 | result = qc_item.split("\n") 35 | if len(result) > max_lines: 36 | return "\n".join(result[:max_lines]) + "\n\n... (truncated)" 37 | else: 38 | return "\n".join(result) 39 | 40 | 41 | def slugify(value): 42 | value = value.lower() 43 | value = re.sub(r"[^a-z0-9]+", "-", value) 44 | value = value.strip("-") 45 | return value 46 | 47 | 48 | def build_wf_pages(): 49 | # import jinja templates 50 | env = Environment( 51 | loader=FileSystemLoader("_templates"), 52 | autoescape=select_autoescape(), 53 | trim_blocks=True, 54 | lstrip_blocks=True, 55 | ) 56 | env.filters["slugify"] = slugify 57 | template = env.get_template("workflow_page.md") 58 | 59 | # import workflow data 60 | with open("../data.js", "r") as f: 61 | next(f) 62 | repos = {} 63 | for repo in json.loads(f.read()): 64 | if repo["standardized"]: 65 | repos[repo["full_name"]] = repo 66 | 67 | # render markdown template with jinja2 for each repo 68 | for current_repo in repos: 69 | repo = repos[current_repo] 70 | wf_data = {} 71 | wf_data["full_name"] = current_repo 72 | # prepare title, description, reporting, qc stats, etc. 73 | wf_data["description"] = repo["description"] 74 | wf_data["topics"] = repo["topics"] 75 | wf_data["linting"] = check_qc_output(repo["linting"]) 76 | wf_data["formatting"] = check_qc_output(repo["formatting"]) 77 | wf_data["release"] = repo["latest_release"] 78 | last_update = datetime.fromtimestamp(repo["updated_at"]) 79 | wf_data["last_update"] = datetime.strftime(last_update, "%Y-%m-%d") 80 | # add deployment options 81 | wf_data["deployment"] = check_deployment(repo["software_stack_deployment"]) 82 | # add configuration from readme; adjust header level if necessary 83 | wf_data["config_from_readme"] = check_readme(repo["config_readme"]) 84 | # render and export 85 | md_rendered = template.render(wf=wf_data) 86 | output_dir = Path(f"docs/workflows/{current_repo.split('/')[0]}") 87 | if not output_dir.exists(): 88 | output_dir.mkdir(parents=True, exist_ok=True) 89 | output_path = output_dir / f"{current_repo.split('/')[1]}.md" 90 | with open(output_path, "w", encoding="utf-8") as f: 91 | f.write(md_rendered) 92 | 93 | # closing statement 94 | print("Workflow pages rendered successfully.") 95 | return None 96 | -------------------------------------------------------------------------------- /source/build_wf_tables.py: -------------------------------------------------------------------------------- 1 | import json 2 | import re 3 | from jinja2 import Environment, FileSystemLoader, select_autoescape 4 | from datetime import datetime 5 | from pathlib import Path 6 | 7 | 8 | # clean repo items, can add more in future 9 | def clean_repo(repo): 10 | if repo["description"] is not None: 11 | repo["description"] = repo["description"].replace('"', "") 12 | if len(repo["description"]) > 100: 13 | repo["description"] = repo["description"][:100] + "..." 14 | else: 15 | repo["description"] = "No description available." 16 | return repo 17 | 18 | 19 | def slugify(value): 20 | value = value.lower() 21 | value = re.sub(r"[^a-z0-9]+", "-", value) 22 | value = value.strip("-") 23 | return value 24 | 25 | 26 | # function to render markdown tables and cards 27 | def render_markdown( 28 | type, 29 | repos, 30 | jinja_env, 31 | template, 32 | output, 33 | metric="stars", 34 | top_n=None, 35 | ): 36 | wf_standard = type == "standardized" 37 | if metric == "stars": 38 | sort_by = "stargazers_count" 39 | reverse = True 40 | elif metric == "update": 41 | sort_by = "updated_at" 42 | reverse = True 43 | elif metric == "watchers": 44 | sort_by = "subscribers_count" 45 | reverse = True 46 | elif metric == "tests": 47 | sort_by = "updated_at" 48 | reverse = True 49 | repos = { 50 | k: v 51 | for k, v in repos.items() 52 | if v["linting"] is None and v["formatting"] is None 53 | } 54 | repos = {k: v for k, v in repos.items() if v["standardized"] == wf_standard} 55 | repos = sorted(repos.values(), key=lambda x: x[sort_by], reverse=reverse) 56 | if top_n: 57 | repos = repos[:top_n] 58 | repos = [clean_repo(repo) for repo in repos] 59 | repos[0]["metric"] = metric 60 | template = jinja_env.get_template(template) 61 | md_rendered = template.render(input=repos) 62 | output_path = Path(output) 63 | with open(output_path, "w", encoding="utf-8") as f: 64 | f.write(md_rendered) 65 | 66 | 67 | def build_wf_tables(): 68 | # items to select from json file 69 | selected_items = [ 70 | "full_name", 71 | "standardized", 72 | "description", 73 | "topics", 74 | "latest_release", 75 | "updated_at", 76 | "linting", 77 | "formatting", 78 | "stargazers_count", 79 | "subscribers_count", 80 | ] 81 | 82 | # import workflow data 83 | with open("../data.js", "r") as f: 84 | next(f) 85 | repos = {} 86 | for repo in json.loads(f.read()): 87 | repo = {k: repo[k] for k in selected_items if k in repo} 88 | repo["user"] = repo["full_name"].split("/")[0] 89 | repo["name"] = repo["full_name"].split("/")[1] 90 | last_update = datetime.fromtimestamp(repo["updated_at"]) 91 | repo["last_update"] = datetime.strftime(last_update, "%Y-%m-%d") 92 | repos[repo["full_name"]] = repo 93 | 94 | # import jinja templates 95 | env = Environment( 96 | loader=FileSystemLoader("_templates"), 97 | autoescape=select_autoescape(), 98 | trim_blocks=True, 99 | lstrip_blocks=True, 100 | ) 101 | env.filters["slugify"] = slugify 102 | 103 | # render tables 104 | for wf_type in ["standardized", "other"]: 105 | render_markdown( 106 | type=wf_type, 107 | repos=repos, 108 | jinja_env=env, 109 | template=f"all_{wf_type}_workflows.md", 110 | output=f"docs/all_{wf_type}_workflows.md", 111 | ) 112 | 113 | # render cards 114 | for metric in ["stars", "watchers", "update", "tests"]: 115 | render_markdown( 116 | type="standardized", 117 | repos=repos, 118 | jinja_env=env, 119 | template="workflows_by.md", 120 | output=f"docs/workflows_by_{metric}.md", 121 | metric=metric, 122 | top_n=15, 123 | ) 124 | 125 | # closing statement 126 | print("Tables and cards rendered successfully.") 127 | return None 128 | -------------------------------------------------------------------------------- /source/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # For the full list of built-in configuration values, see the documentation: 4 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 5 | 6 | # -- Project information ----------------------------------------------------- 7 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information 8 | 9 | project = "snakemake-workflow-catalog" 10 | copyright = "2025, The Snakemake team. " 11 | author = "Johannes Koester, Michael Jahn" 12 | 13 | import sys 14 | import os 15 | 16 | sys.path.insert(0, os.path.abspath(".")) 17 | 18 | from build_wf_pages import build_wf_pages 19 | from build_wf_tables import build_wf_tables 20 | from sphinxawesome_theme.postprocess import Icons 21 | 22 | build_wf_pages() 23 | build_wf_tables() 24 | 25 | # -- General configuration --------------------------------------------------- 26 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration 27 | 28 | extensions = [ 29 | "myst_parser", 30 | "sphinx_design", 31 | "sphinxcontrib.jquery", 32 | "sphinx_datatables", 33 | ] 34 | 35 | templates_path = ["_templates"] 36 | exclude_patterns = [] 37 | 38 | # -- Options for HTML output ------------------------------------------------- 39 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output 40 | 41 | html_theme = "sphinxawesome_theme" 42 | html_static_path = ["_static"] 43 | html_css_files = ["custom.css"] 44 | html_theme_options = { 45 | "logo_light": "_static/logo-snake.svg", 46 | "logo_dark": "_static/logo-snake.svg", 47 | "show_breadcrumbs": True, 48 | "globaltoc_includehidden": True, 49 | "show_prev_next": True, 50 | "main_nav_links": { 51 | "GitHub page": "https://github.com/snakemake/snakemake-workflow-catalog", 52 | "Snakemake homepage": "https://snakemake.github.io", 53 | "Snakemake documentation": "https://snakemake.readthedocs.io", 54 | }, 55 | } 56 | html_title = "Snakemake worklow catalog" 57 | pygments_style = "sphinx" 58 | html_permalinks_icon = Icons.permalinks_icon 59 | suppress_warnings = ["myst.xref_missing", "myst.header"] 60 | myst_enable_extensions = ["colon_fence", "attrs_block"] 61 | myst_heading_anchors = 2 62 | html_sidebars = { 63 | "**": ["globaltoc.html"], 64 | } 65 | 66 | # -- Settings for data-tables plugin ----------------------------------------- 67 | # for all settings see https://datatables.net/reference/option/ 68 | datatables_version = "1.13.4" 69 | datatables_class = "sphinx-datatable" 70 | datatables_options = { 71 | "order": [[4, "desc"]], 72 | } 73 | 74 | # -- Manage redirection of old to new wf pages ------------------------------- 75 | html_js_files = [ 76 | "redirect.js", 77 | ] 78 | -------------------------------------------------------------------------------- /source/docs/about/adding_workflows.md: -------------------------------------------------------------------------------- 1 | 2 | ## Adding workflows 3 | 4 | Workflows are **automatically added** to the Workflow Catalog. This is done by regularly searching Github repositories for matching workflow structures. The catalog includes workflows based on the following criteria. 5 | 6 | ### Generic workflows 7 | 8 | - The workflow is contained in a public Github repository. 9 | - The repository has a `README.md` file, containing the words "snakemake" and "workflow" (case insensitive). 10 | - The repository contains a workflow definition named either `Snakefile` or `workflow/Snakefile`. 11 | - If the repository contains a folder `rules` or `workflow/rules`, that folder must at least contain one file ending on `.smk`. 12 | - The repository is small enough to be cloned into a [Github Actions](https://docs.github.com/en/actions/about-github-actions/understanding-github-actions) job (very large files should be handled via [Git LFS](https://docs.github.com/en/repositories/working-with-files/managing-large-files), so that they can be stripped out during cloning). 13 | - The repository is not blacklisted here. 14 | 15 | ### *Standardized Usage* workflows 16 | 17 | In order to additionally appear in the "standardized usage" area, repositories additionally have to: 18 | 19 | - have their main workflow definition named `workflow/Snakefile` (unlike for [plain inclusion](#generic-workflows), which also allows just `Snakefile` in the root of the repository), 20 | - provide configuration instructions under `config/README.md` 21 | - contain a `YAML` file `.snakemake-workflow-catalog.yml` in their root directory, which configures the usage instructions displayed by this workflow catalog. 22 | 23 | Typical content of the `.snakemake-workflow-catalog.yml` file: 24 | 25 | ```yaml 26 | usage: 27 | mandatory-flags: 28 | desc: # describe your flags here in a few sentences 29 | flags: # put your flags here 30 | software-stack-deployment: 31 | conda: true # whether pipeline works with '--sdm conda' 32 | apptainer: true # whether pipeline works with '--sdm apptainer/singularity' 33 | apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity' 34 | report: true # whether creation of reports using 'snakemake --report report.zip' is supported 35 | ``` 36 | 37 | :::{note} 38 | Definition of mandatory flags can happen through a list of strings (`['--a', '--b']`), or a single string (`'--a --b'`). 39 | ::: 40 | 41 | :::{note} 42 | The content of the `.snakemake-workflow-catalog.yml` file is subject to change. Flags might change in the near future, but current versions will always stay compatible with the catalog. 43 | ::: 44 | 45 | Once included in the standardized usage area you can link directly to the workflow page using the URL `https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows//`. Do not forget to replace the `` and `` tags at the end of the URL. 46 | 47 | ### Release handling 48 | 49 | If your workflow provides Github releases, the catalog will always just scrape the latest non-preview release. Hence, in order to update your workflow's records here, you need to release a new version on Github. 50 | -------------------------------------------------------------------------------- /source/docs/about/contributions.md: -------------------------------------------------------------------------------- 1 | 2 | ## Contributions 3 | 4 | Contributions to the Snakemake Workflow Catalog are welcome! 5 | Ideas can be discussed on the [catalog's Issues page](https://github.com/snakemake/snakemake-workflow-catalog/issues) first, and contributions made through Github Pull Requests. 6 | 7 | ### License 8 | 9 | The Snakemake Workflow Catalog is open-source and available under the [MIT License](https://choosealicense.com/licenses/mit/). 10 | For more information about the individual workflows, browse the [list of *standardized usage* workflows](). 11 | 12 | :::{note} 13 | All workflows collected and presented on the Catalog are licensed under their own terms! 14 | ::: 15 | -------------------------------------------------------------------------------- /source/docs/about/purpose.md: -------------------------------------------------------------------------------- 1 | 2 | ## Purpose 3 | 4 | This repository serves as a centralized collection of workflows designed to facilitate reproducible and scalable data analyses using the [**Snakemake**](https://snakemake.github.io/) workflow management system. 5 | 6 | The Snakemake Workflow Catalog aims to provide a regularly updated list of high-quality workflows that can be easily reused and adapted for various data analysis tasks. By leveraging the power of [**Snakemake**](https://snakemake.github.io/), these workflows promote: 7 | 8 | - **Reproducibility**: Snakemake workflows produce consistent results, making it easier to share and validate scientific findings. 9 | - **Scalability**: Snakemake workflows can be executed on various computing environments, from local machines to high-performance computing clusters and cloud services. 10 | - **Modularity**: Snakemake workflows are structured to allow easy customization and extension, enabling users to adapt them to their specific needs. 11 | -------------------------------------------------------------------------------- /source/docs/about/using_workflows.md: -------------------------------------------------------------------------------- 1 | 2 | ## Using workflows 3 | 4 | ### Basic usage 5 | 6 | To get started with a workflow from the catalog: 7 | 8 | 1. Clone the repository or download the specific workflow directory. 9 | 10 | ```bash 11 | git clone https://github.com// 12 | ``` 13 | 14 | 2. Review the documentation provided with the workflow to understand its requirements and usage. 15 | 16 | 3. Configure the workflow by editing the `config.yml` files as needed. 17 | 18 | 4. Create an environment with access to Snakemake. It is recommended to use `mamba`. 19 | 20 | ```bash 21 | mamba create -n -c snakemake 22 | mamba activate 23 | ``` 24 | 25 | 5. Execute the workflow using Snakemake. 26 | 27 | ```bash 28 | cd 29 | snakemake --cores 2 30 | ``` 31 | 32 | :::{tip} 33 | Use the `--dry-run` option first to check if all inputs are found. 34 | ::: 35 | 36 | For more detailed instructions, please refer to the individual documentation for each [workflow](). 37 | 38 | ### Deployment options 39 | 40 | The deployment method is controlled using the `--software-deployment-method` (short `--sdm`) argument. 41 | 42 | To run the workflow with automatic deployment of all required software via `conda`/`mamba`, use 43 | 44 | ```bash 45 | snakemake --cores all --sdm conda 46 | ``` 47 | 48 | To run the workflow using `apptainer`/`singularity`, use 49 | 50 | ```bash 51 | snakemake --cores all --sdm apptainer 52 | ``` 53 | 54 | To run the workflow using a combination of `conda` and `apptainer`/`singularity` for software deployment, use 55 | 56 | ```bash 57 | snakemake --cores all --sdm conda apptainer 58 | ``` 59 | 60 | Snakemake will automatically detect the main `Snakefile` in the `workflow` subfolder and execute the workflow. 61 | 62 | For further options such as cluster and cloud execution, see [the docs](https://snakemake.readthedocs.io/). 63 | -------------------------------------------------------------------------------- /source/docs/catalog.md: -------------------------------------------------------------------------------- 1 | 2 | # The catalog 3 | 4 | ```{toctree} 5 | :hidden: 6 | ``` 7 | 8 | Here you can find the most important information about the **Snakemake workflow catalog**. 9 | 10 | ```{include} about/purpose.md 11 | ``` 12 | 13 | ```{include} about/using_workflows.md 14 | ``` 15 | 16 | ```{include} about/adding_workflows.md 17 | ``` 18 | 19 | ```{include} about/contributions.md 20 | ``` 21 | -------------------------------------------------------------------------------- /source/docs/snakemake.md: -------------------------------------------------------------------------------- 1 | 2 | # Snakemake 3 | 4 | ```{toctree} 5 | :hidden: 6 | ``` 7 | 8 | ## What is Snakemake? 9 | 10 | The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described *via* a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. 11 | 12 | - To learn more about Snakemake, visit the [Snakemake homepage!](https://snakemake.github.io/) 13 | 14 | - To get an impression of the Snakemake architecture, [read the Snakemake paper](https://doi.org/10.12688/f1000research.29032.2) 15 | 16 | - To learn how to use Snakemake workflows, [read the documentation](https://snakemake.readthedocs.io/en/stable/). 17 | 18 | ## Create your own workflows 19 | 20 | The best starting point to create your own workflows is the [Snakemake workflow template](https://github.com/snakemake-workflows/snakemake-workflow-template). 21 | 22 | The template comes with a pre-configured structure that is compatible with the Snakemake catalog ['standardized usage'](). Just fork or clone the template, start addiong rules and push your workflow to Github. The structure of 'standardized' workflows is like this: 23 | 24 | ``` 25 | ├── config/ 26 | │ └── config.yaml 27 | │ └── README.md 28 | ├── workflow/ 29 | │ ├── Snakefile 30 | │ ├── rules/ 31 | │ ├── scripts/ 32 | │ └── envs/ 33 | ├── .snakemake-workflow-catalog.yml 34 | └── README.md 35 | ``` 36 | 37 | :::{note} 38 | The template is currently not fully functional as it contains no actual `Snakefile` and test cases. This will be changed in the near future. 39 | ::: 40 | 41 | -------------------------------------------------------------------------------- /source/docs/workflows/.gitignore: -------------------------------------------------------------------------------- 1 | *.md 2 | -------------------------------------------------------------------------------- /source/index.md: -------------------------------------------------------------------------------- 1 | ```{toctree} 2 | :caption: Workflows 3 | :maxdepth: 2 4 | :hidden: 5 | 6 | docs/workflows_by_stars 7 | docs/workflows_by_watchers 8 | docs/workflows_by_update 9 | docs/workflows_by_tests 10 | docs/all_standardized_workflows 11 | docs/all_other_workflows 12 | ``` 13 | 14 | ```{toctree} 15 | :caption: About 16 | :maxdepth: 2 17 | :hidden: 18 | 19 | docs/snakemake 20 | docs/catalog 21 | ``` 22 | 23 | # Snakemake workflow catalog 24 | 25 |

28 | 29 | The Snakemake Workflow Catalog aims to provide a regularly updated list of high-quality workflows that can be easily reused and adapted for various data analysis tasks. By leveraging the power of [**Snakemake**](https://snakemake.github.io/), these workflows promote: 30 | 31 | ::::{grid} 3 32 | :::{grid-item-card} **Reproducibility** 33 | Snakemake workflows produce consistent results, making it easier to share and validate scientific findings. 34 |

35 | ::: 36 | :::{grid-item-card} **Scalability** 37 | Snakemake workflows can be executed on various environments, from local machines to clusters and clouds. 38 |

39 | ::: 40 | :::{grid-item-card} **Modularity** 41 | Snakemake workflows allow easy customization and extension, enabling users to adapt them to their needs. 42 |

43 | ::: 44 | :::: 45 | 46 | ## Short cuts 47 | 48 | ::::{grid} 2 49 | :::{grid-item-card} 50 | :columns: auto 51 | ```{button-ref} docs/catalog 52 | :ref-type: myst 53 | :color: primary 54 | Read Introduction - 5 min ⏱️ 55 | ``` 56 | ::: 57 | :::{grid-item-card} 58 | :columns: auto 59 | ```{button-ref} docs/all_standardized_workflows 60 | :ref-type: myst 61 | :color: primary 62 | Explore workflows 🔭 63 | ``` 64 | ::: 65 | :::: 66 | 67 | ## Contributing 68 | 69 | - Improving PRs or issues with the workflow catalog (only the catalog, not the workflows themselves) can be made [here](http://github.com/snakemake/snakemake-workflow-catalog) 70 | - Improving PRs or issues with the listed workflows can be made at the respective workflow repository (see indivuidual [workflow pages]()). 71 | - Resources for creating new workflows can be found [here]() or in more detail on the [Snakemake documnentation](https://snakemake.readthedocs.io/en/stable/index.html) 72 | - New workflows will be [automatically added]() to the workflow catalog if they are contained in eligible Github repositories 73 | -------------------------------------------------------------------------------- /templates/data.js: -------------------------------------------------------------------------------- 1 | var data = 2 | {{ data|tojson(indent=2)|safe }} --------------------------------------------------------------------------------