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Rephrase use/purpose of args variable in modules specifcations #3723

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Rephrase use/purpose of args variable in modules specifcations #3723

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81051b4
Try rephrasing for clarity
jfy133 Jan 22, 2026
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[automated] Fix code linting
nf-core-bot Jan 22, 2026
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jfy133 Jan 23, 2026
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8 changes: 5 additions & 3 deletions sites/docs/src/content/docs/specifications/components/modules/general.md
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,12 @@ Non-file mandatory arguments required for the module to run without error SHOULD

## Optional command arguments

All _non-mandatory_ command-line tool _non-file_ arguments MUST be provided as a string via the `$task.ext.args` variable.
All _non-mandatory_ command-line tool _non-file_ arguments MUST be supported in the module via the `$task.ext.args` variable.

Supply `task.ext.args` from the `modules.config` file by assigning a closure that returns a string to `ext.args`.
The closure allows parameters supplied in a config with `-c` to be updated.
The `$args` variable MUST be placed in the module's tool command to allow optional and/or dynamic variables to be specified by a user or a developer.
The contents of this variable is specified by a pipeline developer or user in with the `ext.args` process variable in a `modules.config` or other Nextflow config file using a closure.
Config file are present in pipelines and subworkflows, not for each individual module, except for configs for tests.
The `$ext.args` variable can also be used in module tests to increase the test coverage of a tool's functionality through a companion `nextflow.config` alongside the test files themselves.

```groovy {2} title="<module>.nf"
script:
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12 changes: 7 additions & 5 deletions sites/docs/src/pages/docs/[subsection].astro
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Expand Up @@ -7,11 +7,13 @@ import { sanitizeNfCoreLabels, addEntriesToSection } from "@utils/functions";
import SidebarSubNav from "@components/sidebar/SidebarSubNav.astro";

export async function getStaticPaths() {
return ["get-started", "users", "developers", "contributors", "specifications", "community", "nf-core-tools"].map((subsection) => ({
params: {
subsection: subsection,
},
}));
return ["get-started", "users", "developers", "contributors", "specifications", "community", "nf-core-tools"].map(
(subsection) => ({
params: {
subsection: subsection,
},
}),
);
}

const { subsection } = Astro.params;
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47 changes: 24 additions & 23 deletions sites/docs/src/pages/docs/index.astro
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Expand Up @@ -109,19 +109,19 @@ const featuredPages = [
title: "What is nf-core?",
href: "/docs/get_started/nf-core",
icon: "octicon:play-16",
description: "Introduction to the nf-core project and community"
description: "Introduction to the nf-core project and community",
},
{
title: "Environment setup",
href: "/docs/get_started/environment_setup/overview",
icon: "octicon:gear-16",
description: "Set up your system to run nf-core pipelines"
description: "Set up your system to run nf-core pipelines",
},
{
title: "Run your first pipeline",
href: "/docs/get_started/run-your-first-pipeline",
icon: "octicon:terminal-16",
description: "Step-by-step guide to running an nf-core pipeline"
description: "Step-by-step guide to running an nf-core pipeline",
},
];

Expand Down Expand Up @@ -174,20 +174,19 @@ const mainSections = [
},
];


// Define training cards
const trainingCards = [
{
title: "Nextflow documentation",
href: "https://www.nextflow.io/docs/latest/index.html",
icon: "octicon:book-16",
description: "Official Nextflow language documentation and guides"
description: "Official Nextflow language documentation and guides",
},
{
title: "Nextflow and nf-core training",
href: "https://training.nextflow.io/latest/",
icon: "octicon:mortar-board-16",
description: "Hands-on training materials and workshops"
description: "Hands-on training materials and workshops",
},
];
---
Expand All @@ -209,15 +208,15 @@ const trainingCards = [
featuredEntries.map((page) => (
<a href={page.href} class="text-decoration-none g-col-12 g-col-md-6 g-col-lg-4">
<div class="card h-100 featured-card">
<div class="card-body">
<div class="featured-icon mb-2">
<Icon name={page.customIcon} />
</div>
<h3 class="h5 card-title mb-2">
{page.metadata?.data.title || page.label}
</h3>
<p class="card-description mb-0">{page.description}</p>
<div class="card-body">
<div class="featured-icon mb-2">
<Icon name={page.customIcon} />
</div>
<h3 class="h5 card-title mb-2">
{page.metadata?.data.title || page.label}
</h3>
<p class="card-description mb-0">{page.description}</p>
</div>
</div>
</a>
))
Expand All @@ -232,7 +231,10 @@ const trainingCards = [
<div class="grid gap-3">
{
mainSections.map((section) => (
<a href={section.sectionHref} class="text-decoration-none g-col-12 g-col-md-6 g-col-lg-4">
<a
href={section.sectionHref}
class="text-decoration-none g-col-12 g-col-md-6 g-col-lg-4"
>
<div class="card h-100 section-card">
<div class="card-body">
<div class="section-icon mb-2">
Expand All @@ -252,21 +254,20 @@ const trainingCards = [
<div class="mb-5">
<h2 class="section-heading mb-2">Additional resources</h2>
<p class="mb-4">
Learn Nextflow and nf-core through comprehensive documentation and hands-on training
materials.
Learn Nextflow and nf-core through comprehensive documentation and hands-on training materials.
</p>
<div class="grid gap-3">
{
trainingCards.map((card) => (
<a href={card.href} class="text-decoration-none g-col-12 g-col-md-6">
<div class="card h-100 featured-card">
<div class="card-body">
<div class="featured-icon mb-2">
<Icon name={card.icon} />
</div>
<h3 class="h5 card-title mb-2">{card.title}</h3>
<p class="card-description mb-0">{card.description}</p>
<div class="card-body">
<div class="featured-icon mb-2">
<Icon name={card.icon} />
</div>
<h3 class="h5 card-title mb-2">{card.title}</h3>
<p class="card-description mb-0">{card.description}</p>
</div>
</div>
</a>
))
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