_book/workflow.html

<!DOCTYPE html>
<html lang="" xml:lang="">
<head>

  <meta charset="utf-8" />
  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
  <title>Chapter 5 Workflow | Introduction to Nextflow</title>
  <meta name="description" content="This is a short tutorial about Nextflow." />
  <meta name="generator" content="bookdown 0.38 and GitBook 2.6.7" />

  <meta property="og:title" content="Chapter 5 Workflow | Introduction to Nextflow" />
  <meta property="og:type" content="book" />
  
  <meta property="og:description" content="This is a short tutorial about Nextflow." />
  <meta name="github-repo" content="rstudio/bookdown-demo" />

  <meta name="twitter:card" content="summary" />
  <meta name="twitter:title" content="Chapter 5 Workflow | Introduction to Nextflow" />
  
  <meta name="twitter:description" content="This is a short tutorial about Nextflow." />
  

<meta name="date" content="2024-04-25" />

  <meta name="viewport" content="width=device-width, initial-scale=1" />
  <meta name="apple-mobile-web-app-capable" content="yes" />
  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
  
  
<link rel="prev" href="processes.html"/>
<link rel="next" href="operators.html"/>
<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />


<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>

<script>
/* ========================================================================
 * Bootstrap: transition.js v3.3.7
 * http://getbootstrap.com/javascript/#transitions
 * ========================================================================
 * Copyright 2011-2016 Twitter, Inc.
 * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
 * ======================================================================== */


+function ($) {
  'use strict';

  // CSS TRANSITION SUPPORT (Shoutout: http://www.modernizr.com/)
  // ============================================================

  function transitionEnd() {
    var el = document.createElement('bootstrap')

    var transEndEventNames = {
      WebkitTransition : 'webkitTransitionEnd',
      MozTransition    : 'transitionend',
      OTransition      : 'oTransitionEnd otransitionend',
      transition       : 'transitionend'
    }

    for (var name in transEndEventNames) {
      if (el.style[name] !== undefined) {
        return { end: transEndEventNames[name] }
      }
    }

    return false // explicit for ie8 (  ._.)
  }

  // http://blog.alexmaccaw.com/css-transitions
  $.fn.emulateTransitionEnd = function (duration) {
    var called = false
    var $el = this
    $(this).one('bsTransitionEnd', function () { called = true })
    var callback = function () { if (!called) $($el).trigger($.support.transition.end) }
    setTimeout(callback, duration)
    return this
  }

  $(function () {
    $.support.transition = transitionEnd()

    if (!$.support.transition) return

    $.event.special.bsTransitionEnd = {
      bindType: $.support.transition.end,
      delegateType: $.support.transition.end,
      handle: function (e) {
        if ($(e.target).is(this)) return e.handleObj.handler.apply(this, arguments)
      }
    }
  })

}(jQuery);
</script>
<script>
/* ========================================================================
 * Bootstrap: collapse.js v3.3.7
 * http://getbootstrap.com/javascript/#collapse
 * ========================================================================
 * Copyright 2011-2016 Twitter, Inc.
 * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
 * ======================================================================== */

/* jshint latedef: false */

+function ($) {
  'use strict';

  // COLLAPSE PUBLIC CLASS DEFINITION
  // ================================

  var Collapse = function (element, options) {
    this.$element      = $(element)
    this.options       = $.extend({}, Collapse.DEFAULTS, options)
    this.$trigger      = $('[data-toggle="collapse"][href="#' + element.id + '"],' +
                           '[data-toggle="collapse"][data-target="#' + element.id + '"]')
    this.transitioning = null

    if (this.options.parent) {
      this.$parent = this.getParent()
    } else {
      this.addAriaAndCollapsedClass(this.$element, this.$trigger)
    }

    if (this.options.toggle) this.toggle()
  }

  Collapse.VERSION  = '3.3.7'

  Collapse.TRANSITION_DURATION = 350

  Collapse.DEFAULTS = {
    toggle: true
  }

  Collapse.prototype.dimension = function () {
    var hasWidth = this.$element.hasClass('width')
    return hasWidth ? 'width' : 'height'
  }

  Collapse.prototype.show = function () {
    if (this.transitioning || this.$element.hasClass('in')) return

    var activesData
    var actives = this.$parent && this.$parent.children('.panel').children('.in, .collapsing')

    if (actives && actives.length) {
      activesData = actives.data('bs.collapse')
      if (activesData && activesData.transitioning) return
    }

    var startEvent = $.Event('show.bs.collapse')
    this.$element.trigger(startEvent)
    if (startEvent.isDefaultPrevented()) return

    if (actives && actives.length) {
      Plugin.call(actives, 'hide')
      activesData || actives.data('bs.collapse', null)
    }

    var dimension = this.dimension()

    this.$element
      .removeClass('collapse')
      .addClass('collapsing')[dimension](0)
      .attr('aria-expanded', true)

    this.$trigger
      .removeClass('collapsed')
      .attr('aria-expanded', true)

    this.transitioning = 1

    var complete = function () {
      this.$element
        .removeClass('collapsing')
        .addClass('collapse in')[dimension]('')
      this.transitioning = 0
      this.$element
        .trigger('shown.bs.collapse')
    }

    if (!$.support.transition) return complete.call(this)

    var scrollSize = $.camelCase(['scroll', dimension].join('-'))

    this.$element
      .one('bsTransitionEnd', $.proxy(complete, this))
      .emulateTransitionEnd(Collapse.TRANSITION_DURATION)[dimension](this.$element[0][scrollSize])
  }

  Collapse.prototype.hide = function () {
    if (this.transitioning || !this.$element.hasClass('in')) return

    var startEvent = $.Event('hide.bs.collapse')
    this.$element.trigger(startEvent)
    if (startEvent.isDefaultPrevented()) return

    var dimension = this.dimension()

    this.$element[dimension](this.$element[dimension]())[0].offsetHeight

    this.$element
      .addClass('collapsing')
      .removeClass('collapse in')
      .attr('aria-expanded', false)

    this.$trigger
      .addClass('collapsed')
      .attr('aria-expanded', false)

    this.transitioning = 1

    var complete = function () {
      this.transitioning = 0
      this.$element
        .removeClass('collapsing')
        .addClass('collapse')
        .trigger('hidden.bs.collapse')
    }

    if (!$.support.transition) return complete.call(this)

    this.$element
      [dimension](0)
      .one('bsTransitionEnd', $.proxy(complete, this))
      .emulateTransitionEnd(Collapse.TRANSITION_DURATION)
  }

  Collapse.prototype.toggle = function () {
    this[this.$element.hasClass('in') ? 'hide' : 'show']()
  }

  Collapse.prototype.getParent = function () {
    return $(this.options.parent)
      .find('[data-toggle="collapse"][data-parent="' + this.options.parent + '"]')
      .each($.proxy(function (i, element) {
        var $element = $(element)
        this.addAriaAndCollapsedClass(getTargetFromTrigger($element), $element)
      }, this))
      .end()
  }

  Collapse.prototype.addAriaAndCollapsedClass = function ($element, $trigger) {
    var isOpen = $element.hasClass('in')

    $element.attr('aria-expanded', isOpen)
    $trigger
      .toggleClass('collapsed', !isOpen)
      .attr('aria-expanded', isOpen)
  }

  function getTargetFromTrigger($trigger) {
    var href
    var target = $trigger.attr('data-target')
      || (href = $trigger.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') // strip for ie7

    return $(target)
  }


  // COLLAPSE PLUGIN DEFINITION
  // ==========================

  function Plugin(option) {
    return this.each(function () {
      var $this   = $(this)
      var data    = $this.data('bs.collapse')
      var options = $.extend({}, Collapse.DEFAULTS, $this.data(), typeof option == 'object' && option)

      if (!data && options.toggle && /show|hide/.test(option)) options.toggle = false
      if (!data) $this.data('bs.collapse', (data = new Collapse(this, options)))
      if (typeof option == 'string') data[option]()
    })
  }

  var old = $.fn.collapse

  $.fn.collapse             = Plugin
  $.fn.collapse.Constructor = Collapse


  // COLLAPSE NO CONFLICT
  // ====================

  $.fn.collapse.noConflict = function () {
    $.fn.collapse = old
    return this
  }


  // COLLAPSE DATA-API
  // =================

  $(document).on('click.bs.collapse.data-api', '[data-toggle="collapse"]', function (e) {
    var $this   = $(this)

    if (!$this.attr('data-target')) e.preventDefault()

    var $target = getTargetFromTrigger($this)
    var data    = $target.data('bs.collapse')
    var option  = data ? 'toggle' : $this.data()

    Plugin.call($target, option)
  })

}(jQuery);
</script>
<script>
window.initializeCodeFolding = function(show) {

  // handlers for show-all and hide all
  $("#rmd-show-all-code").click(function() {
    $('div.r-code-collapse').each(function() {
      $(this).collapse('show');
    });
  });
  $("#rmd-hide-all-code").click(function() {
    $('div.r-code-collapse').each(function() {
      $(this).collapse('hide');
    });
  });

  // index for unique code element ids
  var currentIndex = 1;

  // select all R code blocks
  var rCodeBlocks = $('pre.sourceCode, pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan');
  rCodeBlocks.each(function() {

   if(!this.className.includes("nohide"))
   {
       // create a collapsable div to wrap the code in
    var div = $('<div class="collapse r-code-collapse"></div>');
    if (show)
      div.addClass('in');
    var id = 'rcode-643E0F36' + currentIndex++;
    div.attr('id', id);
    $(this).before(div);
    $(this).detach().appendTo(div);
    console.log(this.className)
    // add a show code button right above
    var showCodeText = $('<span>' + (show ? 'Hide the code! I am good to go!' : 'Show me the code! Need help!') + '</span>');
    var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
    showCodeButton.append(showCodeText);
    showCodeButton
        .attr('data-toggle', 'collapse')
        .attr('data-target', '#' + id)
        .attr('aria-expanded', show)
        .attr('aria-controls', id);

    var buttonRow = $('<div class="row"></div>');
    var buttonCol = $('<div class="col-md-12"></div>');

    buttonCol.append(showCodeButton);
    buttonRow.append(buttonCol);

    div.before(buttonRow);

    // update state of button on show/hide
    div.on('hidden.bs.collapse', function () {
      showCodeText.text('Show me the code! Need help!');
    });
    div.on('show.bs.collapse', function () {
      showCodeText.text('Hide the code! I am good to go!');
    });
   }
  
  });

}
</script>
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
.row { display: flex; }
.collapse { display: none; }
.in { display:block }
</style>
<script>
$(document).ready(function () {
  window.initializeCodeFolding("show" === "hide");
});
</script>


<style type="text/css">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
  { counter-reset: source-line 0; }
pre.numberSource code > span
  { position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
  { content: counter(source-line);
    position: relative; left: -1em; text-align: right; vertical-align: baseline;
    border: none; display: inline-block;
    -webkit-touch-callout: none; -webkit-user-select: none;
    -khtml-user-select: none; -moz-user-select: none;
    -ms-user-select: none; user-select: none;
    padding: 0 4px; width: 4em;
    color: #aaaaaa;
  }
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
div.sourceCode
  {   }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { color: #008000; } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { color: #008000; font-weight: bold; } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>

<style type="text/css">
  
  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
</style>

<link rel="stylesheet" href="style.css" type="text/css" />
</head>

<body>


  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">

    <div class="book-summary">
      <nav role="navigation">

<ul class="summary">
<li><a href="./">Introduction to Nextflow</a></li>

<li class="divider"></li>
<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a>
<ul>
<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#setting-up-the-environment"><i class="fa fa-check"></i><b>1.1</b> Setting up the environment</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="basic-concepts.html"><a href="basic-concepts.html"><i class="fa fa-check"></i><b>2</b> Basic concepts</a>
<ul>
<li class="chapter" data-level="2.1" data-path="basic-concepts.html"><a href="basic-concepts.html#nextflow-scripting"><i class="fa fa-check"></i><b>2.1</b> Nextflow scripting</a></li>
<li class="chapter" data-level="2.2" data-path="basic-concepts.html"><a href="basic-concepts.html#processes-and-channels"><i class="fa fa-check"></i><b>2.2</b> Processes and channels</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="channels.html"><a href="channels.html"><i class="fa fa-check"></i><b>3</b> Channels</a>
<ul>
<li class="chapter" data-level="3.1" data-path="channels.html"><a href="channels.html#of"><i class="fa fa-check"></i><b>3.1</b> of</a></li>
<li class="chapter" data-level="3.2" data-path="channels.html"><a href="channels.html#frompath"><i class="fa fa-check"></i><b>3.2</b> fromPath</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="processes.html"><a href="processes.html"><i class="fa fa-check"></i><b>4</b> Processes</a>
<ul>
<li class="chapter" data-level="4.1" data-path="processes.html"><a href="processes.html#scriptshellexec"><i class="fa fa-check"></i><b>4.1</b> script|shell|exec</a></li>
<li class="chapter" data-level="4.2" data-path="processes.html"><a href="processes.html#input"><i class="fa fa-check"></i><b>4.2</b> input</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="processes.html"><a href="processes.html#input-each"><i class="fa fa-check"></i><b>4.2.1</b> input each</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="processes.html"><a href="processes.html#output"><i class="fa fa-check"></i><b>4.3</b> Output</a></li>
<li class="chapter" data-level="4.4" data-path="processes.html"><a href="processes.html#directives"><i class="fa fa-check"></i><b>4.4</b> Directives</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="processes.html"><a href="processes.html#publishdir"><i class="fa fa-check"></i><b>4.4.1</b> publishDir</a></li>
<li class="chapter" data-level="4.4.2" data-path="processes.html"><a href="processes.html#tag"><i class="fa fa-check"></i><b>4.4.2</b> tag</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="workflow.html"><a href="workflow.html"><i class="fa fa-check"></i><b>5</b> Workflow</a>
<ul>
<li class="chapter" data-level="5.1" data-path="workflow.html"><a href="workflow.html#subworkflows"><i class="fa fa-check"></i><b>5.1</b> Subworkflows</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="operators.html"><a href="operators.html"><i class="fa fa-check"></i><b>6</b> Operators</a>
<ul>
<li class="chapter" data-level="6.1" data-path="operators.html"><a href="operators.html#collect"><i class="fa fa-check"></i><b>6.1</b> Collect</a></li>
<li class="chapter" data-level="6.2" data-path="operators.html"><a href="operators.html#flatten"><i class="fa fa-check"></i><b>6.2</b> flatten</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="configuration-file.html"><a href="configuration-file.html"><i class="fa fa-check"></i><b>7</b> Configuration file</a>
<ul>
<li class="chapter" data-level="7.1" data-path="configuration-file.html"><a href="configuration-file.html#config-scopes"><i class="fa fa-check"></i><b>7.1</b> Config scopes</a>
<ul>
<li class="chapter" data-level="7.1.1" data-path="configuration-file.html"><a href="configuration-file.html#scope-params"><i class="fa fa-check"></i><b>7.1.1</b> Scope params</a></li>
<li class="chapter" data-level="7.1.2" data-path="configuration-file.html"><a href="configuration-file.html#scope-process"><i class="fa fa-check"></i><b>7.1.2</b> Scope process</a></li>
<li class="chapter" data-level="7.1.3" data-path="configuration-file.html"><a href="configuration-file.html#scope-executor"><i class="fa fa-check"></i><b>7.1.3</b> Scope executor</a></li>
<li class="chapter" data-level="7.1.4" data-path="configuration-file.html"><a href="configuration-file.html#configuration-on-uppmax"><i class="fa fa-check"></i><b>7.1.4</b> Configuration on UPPMAX</a></li>
<li class="chapter" data-level="7.1.5" data-path="configuration-file.html"><a href="configuration-file.html#containers"><i class="fa fa-check"></i><b>7.1.5</b> Containers</a></li>
<li class="chapter" data-level="7.1.6" data-path="configuration-file.html"><a href="configuration-file.html#config-profiles"><i class="fa fa-check"></i><b>7.1.6</b> Config profiles</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="8" data-path="more-examples.html"><a href="more-examples.html"><i class="fa fa-check"></i><b>8</b> More examples:</a>
<ul>
<li class="chapter" data-level="8.1" data-path="more-examples.html"><a href="more-examples.html#two-processes"><i class="fa fa-check"></i><b>8.1</b> Two processes</a></li>
<li class="chapter" data-level="8.2" data-path="more-examples.html"><a href="more-examples.html#two-processes-including-collect"><i class="fa fa-check"></i><b>8.2</b> Two processes including collect</a></li>
<li class="chapter" data-level="8.3" data-path="more-examples.html"><a href="more-examples.html#two-processes-collect-accept-parameters-from-the-user"><i class="fa fa-check"></i><b>8.3</b> Two processes, collect, accept parameters from the user</a></li>
<li class="chapter" data-level="8.4" data-path="more-examples.html"><a href="more-examples.html#three-processes"><i class="fa fa-check"></i><b>8.4</b> Three processes</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="resuming-the-pipeline-command-line-interface.html"><a href="resuming-the-pipeline-command-line-interface.html"><i class="fa fa-check"></i><b>9</b> Resuming the pipeline (Command line interface)</a></li>
<li class="chapter" data-level="10" data-path="assignment-2-nextflow.html"><a href="assignment-2-nextflow.html"><i class="fa fa-check"></i><b>10</b> Assignment 2: Nextflow</a>
<ul>
<li class="chapter" data-level="10.1" data-path="assignment-2-nextflow.html"><a href="assignment-2-nextflow.html#set-up-the-environment"><i class="fa fa-check"></i><b>10.1</b> Set up the environment</a></li>
<li class="chapter" data-level="10.2" data-path="assignment-2-nextflow.html"><a href="assignment-2-nextflow.html#part-1"><i class="fa fa-check"></i><b>10.2</b> Part 1</a></li>
<li class="chapter" data-level="10.3" data-path="assignment-2-nextflow.html"><a href="assignment-2-nextflow.html#part-2"><i class="fa fa-check"></i><b>10.3</b> Part 2</a>
<ul>
<li class="chapter" data-level="10.3.1" data-path="assignment-2-nextflow.html"><a href="assignment-2-nextflow.html#part-2.1-build-an-openms-pipeline"><i class="fa fa-check"></i><b>10.3.1</b> Part 2.1 (Build an OpenMS pipeline)</a></li>
<li class="chapter" data-level="10.3.2" data-path="assignment-2-nextflow.html"><a href="assignment-2-nextflow.html#part-2.2-pca-optional-gives-extra-points"><i class="fa fa-check"></i><b>10.3.2</b> Part 2.2 PCA (optional, gives extra points)</a></li>
</ul></li>
</ul></li>
<li class="divider"></li>
<li>Akshai Parakkal Sreenivasan ( <li><a href="https://caramba.clinic/">Caramba lab</a></li>)</li>
<li>Payam Emami ( <li><a href="https://www.nbis.se/">National Bioinformatics Infrastructure Sweden</a></li>)</li>

</ul>

      </nav>
    </div>

    <div class="book-body">
      <div class="body-inner">
        <div class="book-header" role="navigation">
          <h1>
            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Introduction to Nextflow</a>
          </h1>
        </div>

        <div class="page-wrapper" tabindex="-1" role="main">
          <div class="page-inner">

            <section class="normal" id="section-">
<div id="workflow" class="section level1 hasAnchor" number="5">
<h1><span class="header-section-number">Chapter 5</span> Workflow<a href="workflow.html#workflow" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Workflow connects process and channels together. The dataflow logic is executed here. The workflow definition starts with the keyword <code>workflow</code>, followed by an optional name, and finally the workflow body delimited by curly braces. The logic is written inside the curly bracket. The order in which a task is executed is determined only by its dependencies, so a task will be executed as soon as all of its required inputs are available.</p>
<div class="sourceCode" id="cb44"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb44-1"><a href="workflow.html#cb44-1"></a><span class="ex">workflow</span> workflowname{</span>
<span id="cb44-2"><a href="workflow.html#cb44-2"></a><span class="ex">output_channel1</span> = example_workflow<span class="er">(</span><span class="kw">)</span></span>
<span id="cb44-3"><a href="workflow.html#cb44-3"></a><span class="ex">output_channel2</span> = example_workflow2<span class="er">(</span><span class="ex">output_channel1</span><span class="kw">)</span></span>
<span id="cb44-4"><a href="workflow.html#cb44-4"></a><span class="fu">output_channel2.view()</span></span>
<span id="cb44-5"><a href="workflow.html#cb44-5"></a><span class="er">}</span></span></code></pre></div>
<p>Channels can be passed and received in the workflow using</p>
<div class="sourceCode" id="cb45"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb45-1"><a href="workflow.html#cb45-1"></a><span class="ex">workflow</span> {</span>
<span id="cb45-2"><a href="workflow.html#cb45-2"></a><span class="ex">output_channel</span> = example_workflow<span class="er">(</span><span class="ex">input_channel</span><span class="kw">)</span></span>
<span id="cb45-3"><a href="workflow.html#cb45-3"></a><span class="er">}</span></span></code></pre></div>
<p>Operators can be applied to the input or output channel. For example</p>
<div class="sourceCode" id="cb46"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb46-1"><a href="workflow.html#cb46-1"></a><span class="ex">workflow</span> {</span>
<span id="cb46-2"><a href="workflow.html#cb46-2"></a><span class="ex">output_channel</span> = example_workflow<span class="er">(</span><span class="ex">input_channel</span><span class="kw">)</span><span class="fu">.collect()</span> <span class="ex">//</span> <span class="co">#1</span></span>
<span id="cb46-3"><a href="workflow.html#cb46-3"></a><span class="er">}</span></span></code></pre></div>
<ol style="list-style-type: decimal">
<li>Operator <code>collect()</code> is applied to the data coming from the process <code>example_workflow</code></li>
</ol>
<p>Multiple channels can be provided as input and also received as</p>
<div class="sourceCode" id="cb47"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb47-1"><a href="workflow.html#cb47-1"></a><span class="ex">workflow</span> {</span>
<span id="cb47-2"><a href="workflow.html#cb47-2"></a><span class="kw">(</span><span class="ex">output_channel1,output_channel2</span><span class="kw">)</span> <span class="ex">=</span> example_workflow<span class="er">(</span><span class="ex">input_channel1,input_channel2</span><span class="kw">)</span></span>
<span id="cb47-3"><a href="workflow.html#cb47-3"></a><span class="er">}</span></span></code></pre></div>
<div id="subworkflows" class="section level2 hasAnchor" number="5.1">
<h2><span class="header-section-number">5.1</span> Subworkflows<a href="workflow.html#subworkflows" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>A named workflow is a “subworkflow” that can be invoked from other workflows. For example:</p>
<div class="sourceCode" id="cb48"><pre class="sourceCode numberSource bash nohide numberLines"><code class="sourceCode bash"><span id="cb48-1"><a href="workflow.html#cb48-1"></a><span class="ex">workflow</span> my_pipeline { // <span class="co">#1</span></span>
<span id="cb48-2"><a href="workflow.html#cb48-2"></a>    <span class="fu">foo()</span></span>
<span id="cb48-3"><a href="workflow.html#cb48-3"></a>    <span class="ex">bar</span><span class="er">(</span> <span class="fu">foo.out.collect()</span> <span class="kw">)</span></span>
<span id="cb48-4"><a href="workflow.html#cb48-4"></a><span class="er">}</span></span>
<span id="cb48-5"><a href="workflow.html#cb48-5"></a></span>
<span id="cb48-6"><a href="workflow.html#cb48-6"></a><span class="ex">workflow</span> {</span>
<span id="cb48-7"><a href="workflow.html#cb48-7"></a>    <span class="fu">my_pipeline()</span></span>
<span id="cb48-8"><a href="workflow.html#cb48-8"></a><span class="er">}</span></span></code></pre></div>
<ol style="list-style-type: decimal">
<li>Name of the subworkflow here is <code>my_pipeline</code></li>
</ol>
</div>
</div>
            </section>

          </div>
        </div>
      </div>
<a href="processes.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
<a href="operators.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
    </div>
  </div>
<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
<script>
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": true,
"twitter": true,
"linkedin": false,
"weibo": false,
"instapaper": false,
"vk": false,
"whatsapp": false,
"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
},
"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
},
"edit": {
"link": null,
"text": null
},
"history": {
"link": null,
"text": null
},
"view": {
"link": null,
"text": null
},
"download": ["_main.pdf", "_main.epub"],
"search": {
"engine": "fuse",
"options": null
},
"toc": {
"collapse": "subsection"
}
});
});
</script>

</body>

</html>