Merge branch '251117-module-system' into 251117-module-system-implementation

Author: jorgee

VERSION

@@ -1 +1 @@
-26.01.0-edge
+26.01.1-edge

changelog.txt

@@ -1,5 +1,14 @@
 NEXTFLOW CHANGE-LOG
 ===================
+26.01.1-edge - 11 Feb 2026
+- Add OSC 8 hyperlinks to task hashes in progress output (#6799) [8d266c76b]
+- Fix JGit resources not being closed in CLI commands (#6795) [908e4c70d]
+- Fix listDirectory() to follow symbolic links (#6821) [1ee59b3d0]
+- Improve documentation of workflow outputs (#6822) [3f6c6b351]
+- Bump ch.qos.logback@1.5.26 — fix false version mismatch warning in shadow JAR [0b97f4a84]
+- Bump ch.qos.logback@1.5.25 (CVE-2026-1225) [97dec3af6]
+- Bump com.gradleup.shadow@9.3.1 (CVE-2025-68161) [d31e6edc7]
+
 26.01.0-edge - 8 Feb 2026
 - Add accelerator request to trace record (#6703) [00f35b3a9]
 - Add aws.batch.forceGlacierTransfer config option (#6700) [e3bf3153b]

docs/_static/theme.css

@@ -244,3 +244,13 @@ div.deprecated p:first-child::before     { color: #C3514D; }
     font-size: 0.7rem;
     margin-left: 0.5rem;
 }
+
+/* Site-wide announcement banner */
+.admonition.site-banner {
+    background: #E2F7F3;
+    border-left: none;
+}
+
+.admonition.site-banner .admonition-title {
+    background: #0CAE8E;
+}

docs/_templates/layout.html

@@ -1,5 +1,13 @@
 {% extends "!layout.html" %}
 
+{% block document %}
+    <div class="admonition site-banner" style="background: #E2F7F3; border-left: none;">
+        <p class="admonition-title" style="background: #0CAE8E;">Nextflow documentation is migrating</p>
+        <p>Nextflow documentation is being migrated to <a href="https://docs.seqera.io/nextflow/">docs.seqera.io/nextflow</a>. This site will remain available throughout the migration.</p>
+    </div>
+    {{ super() }}
+{% endblock %}
+
 {% block sidebartitle %}
     {{ super() }}
     {%- set version_selected = "stable" -%}

docs/azure.md

@@ -573,14 +573,14 @@ By default, Nextflow creates pool nodes suitable for most bioinformatics workloa
 
 Below are example configurations for common operating systems used in scientific computing:
 
-**Ubuntu 22.04 (default)**
+**Ubuntu 24.04 (default)**
 
 ```groovy
 azure {
     batch {
         pools {
             <POOL_NAME> {
-                sku = "batch.node.ubuntu 22.04"
+                sku = "batch.node.ubuntu 24.04"
                 offer = "ubuntu-hpc"
                 publisher = "microsoft-dsvm"
             }

docs/migrations/25-10.md

@@ -201,7 +201,7 @@ export NXF_PLUGINS_REGISTRY_URL="https://raw.githubusercontent.com/nextflow-io/p
 ```
 
 :::{note}
-Plugin developers will not be able to submit PRs to the legacy plugin index once the plugin registry is generally available. Plugins should be updated to publish to the Nextflow plugin registry using the {ref}`Nextflow Gradle plugin <gradle-plugin-page>` instead. See {ref}`plugin-registry-page` for details.
+Plugins should be updated to publish to the Nextflow plugin registry using the {ref}`Nextflow Gradle plugin <gradle-plugin-page>` instead of the legacy plugin index. See {ref}`plugin-registry-page` for details.
 :::
 
 <h3>New syntax for workflow handlers</h3>

docs/reference/config.md

@@ -113,7 +113,7 @@ The following settings are available:
 : The AWS Batch [Execution Role](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) ARN that needs to be used to execute the Batch Job. It is mandatory when using AWS Fargate.
 
 `aws.batch.forceGlacierTransfer`
-: :::{versionadded 26.04.0}
+: :::{versionadded} 26.04.0 
   :::
 : When `true`, add the `--force-glacier-transfer` flag to AWS CLI S3 download commands (default: `false`).
 : This option is needed when staging directories that have been restored from [S3 Glacier](https://aws.amazon.com/s3/storage-classes/glacier/). It does not restore objects from Glacier.

docs/reference/stdlib-types.md

@@ -600,10 +600,10 @@ The following methods are available for writing to files:
 : Appends text to a file without replacing existing content.
 
 `setText( text: String )`
-: Writes text to a file. Equivalent to setting the `text` property.
+: Writes text to a file, replacing any existing content. Equivalent to setting the `text` property.
 
 `write( text: String )`
-: Writes a string to a file, replacing any existing content.
+: Writes text to a file, replacing any existing content. Equivalent to `setText()`.
 
 <h3>Filesystem operations</h3>
 

docs/strict-syntax.md

@@ -585,6 +585,8 @@ export NXF_SYNTAX_PARSER=v2
 
 See {ref}`Configuration <config-syntax>` for a comprehensive description of the configuration language.
 
+### Mixing config statements and scripting statements
+
 Currently, Nextflow parses config files as Groovy scripts, allowing the use of scripting constructs like variables, helper functions, try-catch blocks, and conditional logic for dynamic configuration:
 
 ```groovy
@@ -625,12 +627,32 @@ Each conditional configuration is defined in a separate config file:
 // small.config
 params.max_memory = 32.GB
 params.max_cpus = 8
+```
 
+```groovy
 // large.config
 params.max_memory = 128.GB
 params.max_cpus = 32
 ```
 
+### Referencing config settings as variables
+
+The legacy parser allows config settings to be referenced like variables:
+
+```groovy
+google.location = "us-west1"
+google.batch.subnetwork = "regions/${google.location}/subnetworks/default"
+```
+
+The strict config syntax does not support this. Only params can be referenced as variables:
+
+```groovy
+params.location = "us-west1"
+
+google.location = params.location
+google.batch.subnetwork = "regions/${params.location}/subnetworks/default"
+```
+
 ## Preserving Groovy code
 
 There are two ways to preserve Groovy code: