From 81051b4949a97fc42f78ce035adfcb9560d17dd8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 22 Jan 2026 11:37:57 +0100 Subject: [PATCH 1/4] Try rephrasing for clarity --- .../docs/specifications/components/modules/general.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/sites/docs/src/content/docs/specifications/components/modules/general.md b/sites/docs/src/content/docs/specifications/components/modules/general.md index 529c2f8a69..50787021cb 100644 --- a/sites/docs/src/content/docs/specifications/components/modules/general.md +++ b/sites/docs/src/content/docs/specifications/components/modules/general.md @@ -18,10 +18,11 @@ 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 `$task.ext.args` variable. +All _non-mandatory_ command-line tool _non-file_ arguments MUST supported in the module via the `$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 `$args` variable MUST be placed in the module's tool command to allow optional and/or dynamic variables to be specified by a user or a developer. +The contents of this variable is specified by a pipeline developer or user in with the `ext.args` process variable in a `modules.config` or other Nextflow config file using a closure. +The `$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=".nf" script: From b3b7d93e4994c82b0ed2962e8dc0c5f655e796ce Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 22 Jan 2026 10:44:58 +0000 Subject: [PATCH 2/4] [automated] Fix code linting --- sites/docs/src/pages/docs/[subsection].astro | 12 ++--- sites/docs/src/pages/docs/index.astro | 47 ++++++++++---------- 2 files changed, 31 insertions(+), 28 deletions(-) diff --git a/sites/docs/src/pages/docs/[subsection].astro b/sites/docs/src/pages/docs/[subsection].astro index c5e3e14678..24aad12dcf 100644 --- a/sites/docs/src/pages/docs/[subsection].astro +++ b/sites/docs/src/pages/docs/[subsection].astro @@ -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; diff --git a/sites/docs/src/pages/docs/index.astro b/sites/docs/src/pages/docs/index.astro index f23def7839..fd04a2bcce 100644 --- a/sites/docs/src/pages/docs/index.astro +++ b/sites/docs/src/pages/docs/index.astro @@ -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", }, ]; @@ -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", }, ]; --- @@ -209,15 +208,15 @@ const trainingCards = [ featuredEntries.map((page) => (
-
-
- -
-

- {page.metadata?.data.title || page.label} -

-

{page.description}

+
+
+
+

+ {page.metadata?.data.title || page.label} +

+

{page.description}

+
)) @@ -232,7 +231,10 @@ const trainingCards = [
{ mainSections.map((section) => ( - +
@@ -252,21 +254,20 @@ const trainingCards = [

Additional resources

- 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.

{ trainingCards.map((card) => (
-
-
- -
-

{card.title}

-

{card.description}

+
+
+
+

{card.title}

+

{card.description}

+
)) From 21312f6e2deab53357c03c180badb9855956a2b5 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 23 Jan 2026 08:43:27 +0100 Subject: [PATCH 3/4] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .../content/docs/specifications/components/modules/general.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sites/docs/src/content/docs/specifications/components/modules/general.md b/sites/docs/src/content/docs/specifications/components/modules/general.md index 50787021cb..ee58943f67 100644 --- a/sites/docs/src/content/docs/specifications/components/modules/general.md +++ b/sites/docs/src/content/docs/specifications/components/modules/general.md @@ -18,7 +18,7 @@ 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 supported in the module 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. The `$args` variable MUST be placed in the module's tool command to allow optional and/or dynamic variables to be specified by a user or a developer. The contents of this variable is specified by a pipeline developer or user in with the `ext.args` process variable in a `modules.config` or other Nextflow config file using a closure. From 0f5d79aac354be776677e56207955aed7e81f12b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 23 Jan 2026 08:45:21 +0100 Subject: [PATCH 4/4] Apply suggestion from @jfy133 --- .../content/docs/specifications/components/modules/general.md | 1 + 1 file changed, 1 insertion(+) diff --git a/sites/docs/src/content/docs/specifications/components/modules/general.md b/sites/docs/src/content/docs/specifications/components/modules/general.md index ee58943f67..7185a41a21 100644 --- a/sites/docs/src/content/docs/specifications/components/modules/general.md +++ b/sites/docs/src/content/docs/specifications/components/modules/general.md @@ -22,6 +22,7 @@ All _non-mandatory_ command-line tool _non-file_ arguments MUST be supported in The `$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=".nf"