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<!doctype html>
<html lang="en">
<head>
<!-- Required meta tags -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.5.3/dist/css/bootstrap.min.css" integrity="sha384-TX8t27EcRE3e/ihU7zmQxVncDAy5uIKz4rEkgIXeMed4M0jlfIDPvg6uqKI2xXr2" crossorigin="anonymous">
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">
<link rel="stylesheet" href="https://unpkg.com/bootstrap-table@1.18.1/dist/bootstrap-table.min.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/prism/1.23.0/themes/prism.min.css" integrity="sha512-tN7Ec6zAFaVSG3TpNAKtk4DOHNpSwKHxxrsiw4GHKESGPs5njn/0sMCUMl2svV4wo4BK/rCP7juYz+zx+l6oeQ==" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/prism/1.23.0/plugins/toolbar/prism-toolbar.min.css" integrity="sha512-DSAA0ziYwggOJ3QyWFZhIaU8bSwQLyfnyIrmShRLBdJMtiYKT7Ju35ujBCZ6ApK3HURt34p2xNo+KX9ebQNEPQ==" crossorigin="anonymous"
/>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.4.1/font/bootstrap-icons.css">
<style>
#content {
margin-top: 2em;
margin-left: auto;
margin-right: auto;
width: 90%;
}
#logo {
height: 2em;
vertical-align: center;
}
pre#check-msg {
overflow: auto;
max-height: 80vh;
}
.navbar a:not(.navbar-brand) {
color: #007bff !important;
}
#repos tr td:nth-child(1) a {
opacity: 0.5;
transition: opacity 0.2s ease-in-out;
}
#repos tr:hover td:nth-child(1) a {
opacity: 1.0;
}
#config-readme h1 {
font-size: 1.5rem;
}
#config-readme h2 {
font-size: 1.4rem;
}
#config-readme h3 {
font-size: 1.3rem;
}
#config-readme h4 {
font-size: 1.2rem;
}
#config-readme h5 {
font-size: 1.1rem;
}
</style>
<title>Snakemake workflow catalog</title>
</head>
<body>
<!-- Image and text -->
<!-- Image and text -->
<nav class="navbar navbar-light bg-light">
<a class="navbar-brand" href="#">
<img src="logo-snake.svg" id="logo" /> Snakemake workflow catalog
</a>
<div class="navbar-nav">
<div class="navbar-text">A comprehensive catalog of
<a href="#" data-toggle="modal" data-target="#rule-popup">standards compliant</a>, public, <a href="https://snakemake.github.io">Snakemake</a> workflows
</div>
</div>
</nav>
<div id="content">
<ul class="nav nav-tabs" role="tablist">
<li class="nav-item">
<a class="nav-link active" id="standardized-tab" data-toggle="tab" href="#standardized" role="tab" aria-controls="standardized" aria-selected="true">Standardized usage <span class="badge badge-primary" id="standardized-workflow-count-badge"></span></a>
</li>
<li class="nav-item">
<a class="nav-link" id="all-tab" data-toggle="tab" href="#all" role="tab" aria-controls="all" aria-selected="false">All workflows <span class="badge badge-primary" id="workflow-count-badge"></span></a>
</li>
</ul>
<table id="repos" data-toggle="table" data-pagination="true" data-search="true" data-pagination="true" data-sort-name="stargazers_count" data-sort-order="desc" data-classes="table">
<thead>
<tr>
<th data-field="usage" data-formatter="usage_formatter"> </th>
<th data-searchable="true" data-sortable="true" data-field="full_name" data-formatter="name_formatter">
Workflow</th>
<th data-searchable="true" data-field="description">Description</th>
<th data-searchable="true" data-field="topics" data-formatter="topics_formatter">Topics</th>
<th data-field="full_name" data-formatter="qc_formatter">QC</td>
<th data-sortable="true" data-field="stargazers_count" data_formatter="stargazers_formatter">Stars</th>
<th data-sortable="true" data-field="subscribers_count" data_formatter="watchers_formatter">Watchers</th>
</tr>
</thead>
<tbody></tbody>
</table>
</div>
<hr/>
<div class="footer">
<p>
<small>
<a href="https://github.com/snakemake">© 2020 The Snakemake team</a>
</small>
</p>
<p>
<small>This catalog is generated automatically by querying Github APIs; the Snakemake team is not responsible for
the linked workflows.</small>
</p>
<p>
<small>Source code: <a
href="https://github.com/snakemake/snakemake-workflow-catalog">https://github.com/snakemake/snakemake-workflow-catalog</a>
</small>
</p>
</div>
<div class="modal fade" tabindex="-1" role="dialog" id="detail-popup">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Modal title</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<pre id="check-msg"></pre>
</div>
</div>
</div>
</div>
<div class="modal fade" tabindex="-1" role="dialog" id="usage-popup">
<div class="modal-dialog modal-lg modal-dialog-scrollable" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Workflow</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<table data-classes="table" id="repo-info-table">
<thead>
<tr>
<th data-searchable="true" data-field="description">Description</th>
<th data-searchable="true" data-field="topics" data-formatter="topics_formatter">Topics</th>
<th data-field="full_name" data-formatter="qc_formatter">QC</td>
<th data-sortable="true" data-field="stargazers_count" data_formatter="stargazers_formatter">Stars</th>
<th data-sortable="true" data-field="subscribers_count" data_formatter="watchers_formatter">Watchers</th>
</tr>
</thead>
<tbody></tbody>
</table>
<div id="accordion">
<div class="card">
<div class="card-header" id="setup-snakemake">
<h5 class="mb-0">
<button class="btn btn-link" data-toggle="collapse" data-target="#collapseOne" aria-expanded="true" aria-controls="collapseOne">
Step 1: install Snakemake and Snakedeploy
</button>
</h5>
</div>
<div id="collapseOne" class="collapse show" aria-labelledby="headingOne" data-parent="#accordion">
<div class="card-body">
<p>
Snakemake and Snakedeploy are best installed via the <a href="https://github.com/mamba-org/mamba">Mamba package manager</a> (a drop-in replacement for conda). If you have neither Conda nor Mamba, it can be installed
via <a href="https://github.com/conda-forge/miniforge#mambaforge">Mambaforge</a>. For other options see <a href="https://github.com/mamba-org/mamba">here</a>.
</p>
<p>
Given that Mamba is installed, run
<pre><code class="language-bash">mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy</code></pre> to install both Snakemake and Snakedeploy in an isolated environment. For all following
commands ensure that this environment is activated via
</p>
<p>
<pre><code class="language-bash">conda activate snakemake</code></pre>
</p>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="deploy-workflow">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseTwo" aria-expanded="false" aria-controls="collapseTwo">
Step 2: deploy workflow
</button>
</h5>
</div>
<div id="collapseTwo" class="collapse" aria-labelledby="headingTwo" data-parent="#accordion">
<div class="card-body">
<p>
Given that Snakemake and Snakedeploy are installed and available (see Step 1), the workflow can be deployed as follows.
</p>
<p>
First, create an appropriate project working directory on your system and enter it:
<pre><code class="language-bash">mkdir -p path/to/project-workdir
cd path/to/project-workdir</code></pre> In all following steps, we will assume that you are inside of that directory.
</p>
<p>
Second, run
<pre><code id="snakedeploy-cmd" class="language-bash"></code></pre> Snakedeploy will create two folders <code>workflow</code> and <code>config</code>. The former contains the deployment of the chosen workflow as
a <a href="https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-and-combining-pre-exising-workflows">Snakemake module</a>, the latter contains configuration files which will be modified in
the next step in order to configure the workflow to your needs. Later, when executing the workflow, Snakemake will automatically find the main <code>Snakefile</code> in the <code>workflow</code> subfolder.
</p>
Third, consider to put this directory under version control, e.g. by <a href="https://docs.github.com/en/github/importing-your-projects-to-github/adding-an-existing-project-to-github-using-the-command-line">managing
it via a (private) Github repository</a>
</p>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="configure-workflow">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseThree" aria-expanded="false" aria-controls="collapseThree">
Step 3: configure workflow
</button>
</h5>
</div>
<div id="collapseThree" class="collapse" aria-labelledby="headingThree" data-parent="#accordion">
<div class="card-body">
<div id="config-readme"></div>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="run-workflow">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseFour" aria-expanded="false" aria-controls="collapseFour">
Step 4: run workflow
</button>
</h5>
</div>
<div id="collapseFour" class="collapse" aria-labelledby="headingFour" data-parent="#accordion">
<div class="card-body" id="run-workflow-content"></div>
</div>
</div>
<div class="card">
<div class="card-header" id="generate-report">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseFive" aria-expanded="false" aria-controls="collapseFive">
Step 5: generate report
</button>
</h5>
</div>
<div id="collapseFive" class="collapse" aria-labelledby="headingFive" data-parent="#accordion">
<div class="card-body" id="generate-report-content">
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 via
<pre><code class="language-bash">snakemake --report report.zip</code></pre> The resulting <code>report.zip</code> file can be passed on to collaborators, provided as a supplementary file in publications, or uploaded
to a service like <a href="https://zenodo.org">Zenodo</a> in order to obtain a citable <a href="https://en.wikipedia.org/wiki/Digital_object_identifier">DOI</a>.
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="modal fade" tabindex="-1" role="dialog" id="rule-popup">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Rules for inclusion
<a data-toggle="tooltip" data-placement="top" title="URL to display this dialog" href="https://snakemake.github.io/snakemake-workflow-catalog?rules=true">
<i class="bi bi-link"></i>
</a>
</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<h5>All workflows</h5>
<p>
This catalog includes workflows based on the following criteria:
<ul>
<li>The workflow is contained in a public <a href="https://github.com">Github</a> repository.</li>
<li>The repository has a readme, containing the words "snakemake" and "workflow" (case insensitive).</li>
<li>The repository contains a workflow definition named either <code>Snakefile</code> or
<code>workflow/Snakefile</code>.
</li>
<li>If the repository contains a folder <code>rules</code> or <code>workflow/rules</code> that folder must at least contain one file ending on <code>.smk</code>.</li>
<li>The repository is small enough to be cloned into a Github actions job (very large files should be handled via Git LFS, so that they can be stripped out during cloning).</li>
<li>The repository is not blacklisted <a href="https://github.com/snakemake/snakemake-workflow-catalog/blob/main/blacklist.txt">here</a>.</li>
</ul>
</p>
<h5>Standardized usage</h5>
<p>
In order to additionally appear in the "standardized usage" area, repositories additionally have to
<ul>
<li>have their main workflow definition named <code>workflow/Snakefile</code> (unlike for plain inclusion (see above), which also allows just <code>Snakefile</code> in the root of the repository),</li>
<li>provide configuration instructions under <code>config/README.md</code>,</li>
<li>
contain a <a href="https://yaml.org">YAML</a> file <code>.snakemake-workflow-catalog.yml</code> in their root directory, which configures the usage instructions displayed by this workflow catalog.
<pre><code class="language-yaml">
usage:
mandatory-flags: # optional definition of additional flags
desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
flags: # put your flags here
software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
conda: true # whether pipeline works with --use-conda
singularity: true # whether pipeline works with --use-singularity
singularity+conda: true # whether pipeline works with --use-singularity --use-conda
report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations
</code></pre>
</li>
</ul>
</p>
<p>
Once included in the standardized usage area you can link directly to the usage instructions for your repository via the URL <code>https://snakemake.github.io/snakemake-workflow-catalog?usage=<owner>/<repo></code>.
</p>
<h5>Release handling</h5>
If your workflow provides Github releases, we 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.
</div>
</div>
</div>
</div>
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return `
<a href="#" data-msg="${escapeHtml(msg)}" data-title="${check} errors" data-toggle="modal" data-target="#detail-popup">
<img src="https://img.shields.io/badge/${check}-${passed}-${color}" />
</a>
`
}
function qc_formatter(_, repo) {
return `
<img src="https://img.shields.io/github/license/${repo.full_name}" /><br />
<a href="https://github.com/${repo.full_name}/commits"><img src="https://img.shields.io/github/last-commit/${repo.full_name}" /></a><br />
${check_badge("linting", repo.linting)}<br />
${check_badge("formatting", repo.formatting)}
`
}
function stargazers_formatter(_, repo) {
return `<a href="https://github.com/${repo.full_name}/stargazers">${repo.stargazers_count}</a>`
}
function watchers_formatter(_, repo) {
return `<a href="https://github.com/${repo.full_name}/watchers">${repo.subscribers_count}</a>`
}
function get_repo_row(full_name) {
for (row of data) {
if (row.full_name == full_name) {
return row
}
}
}
function render_usage_modal(rowdata) {
var repo_url = get_repo_url(rowdata.full_name)
var flags = ""
if (rowdata.mandatory_flags && rowdata.mandatory_flags.flags) {
flags = rowdata.mandatory_flags.flags
}
var modal = $("#usage-popup")
modal
.find(".modal-title")
.empty()
.append($(`<span><a href=${repo_url}>${rowdata.full_name}</a></span> <a data-toggle="tooltip" data-placement="top" title="URL to display this repository" href="https://snakemake.github.io/snakemake-workflow-catalog?repo=${rowdata.full_name}"><i class="bi bi-link"></i></a>`))
$("#repo-info-table").bootstrapTable({
data: [rowdata]
})
$("#repo-info-table").bootstrapTable("load", [rowdata])
var method_flags = {
"conda": "--use-conda",
"singularity": "--use-singularity",
"singularity+conda": "--use-conda --use-singularity"
}
var deployment_methods = {}
for (const method in rowdata.software_stack_deployment) {
if (rowdata.software_stack_deployment[method]) {
deployment_methods[method] = `snakemake --cores all ${method_flags[method]} ${flags}`
}
}
modal
.find("#run-workflow-content")
.empty()
.append(nunjucks.render("templates/run-instructions.html.njk", {
"deployment_methods": deployment_methods
}))
modal
.find('#snakedeploy-cmd')
.text(`snakedeploy deploy-workflow ${repo_url} . --tag ${rowdata.latest_release}`)
modal
.find('#config-readme')
.empty()
.append($(rowdata.config_readme))
}
$("#repos").bootstrapTable({
data: data
})
// show number of workflows
var nrows = $("#repos")
.bootstrapTable('getOptions')
.totalRows
$("#workflow-count-badge")
.text(nrows)
// filter to standardized by default
$("#repos").bootstrapTable("filterBy", {
standardized: [true]
})
// show number of standardized workflows
var nrows_standardized = $("#repos")
.bootstrapTable('getOptions')
.totalRows
$("#standardized-workflow-count-badge")
.text(nrows_standardized)
$('#detail-popup').on('show.bs.modal', function(event) {
var source = $(event.relatedTarget) // item that triggered the modal
var msg = source.data('msg')
var title = source.data('title')
var modal = $(this)
modal
.find('.modal-title')
.text(title)
modal
.find('.modal-body pre')
.text(msg)
})
$('#usage-popup').on('show.bs.modal', function(event) {
var source = $(event.relatedTarget) // item that triggered the modal
var rowdata = source.data('row')
if (rowdata != undefined) {
// rowdata is present when triggered via button
render_usage_modal(rowdata)
}
})
$("#standardized-tab").on("click", function(e) {
e.preventDefault()
$("#repos").bootstrapTable("filterBy", {
standardized: [true]
})
})
$("#all-tab").on("click", function(e) {
e.preventDefault()
$("#repos").bootstrapTable("filterBy", {
standardized: [undefined, false, true]
})
})
// handle directly linking to usage popup
var search_params = new URLSearchParams(window.location.search)
if (search_params.has("usage")) {
render_usage_modal(get_repo_row(search_params.get("usage")))
$("#usage-popup").modal()
}
if (search_params.has("repo")) {
render_usage_modal(get_repo_row(search_params.get("repo")))
$("#usage-popup").modal()
}
// handle directly linking to rules
if (search_params.has("rules")) {
$("#rule-popup").modal()
}
</script>
</body>
</html>