Merge branch 'master' into more-gha-updates

Signed-off-by: GitHub <noreply@github.com>

Co-authored-by: ewels <465550+ewels@users.noreply.github.com>

Author: Copilot

.github/workflows/build.yml

@@ -26,6 +26,7 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
+
 jobs:
   build:
     name: Build
@@ -256,6 +257,10 @@ jobs:
     permissions:
       contents: write
     steps:
+      # Intentionally persists credentials: the `release` task in
+      # packing.gradle runs `git push` and `git push origin vX.Y.Z` against
+      # this repo; both rely on actions/checkout having written the token
+      # into .git/config as http.extraheader.
       - name: Checkout
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:

.github/workflows/docs.yml

@@ -13,6 +13,7 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
+
 jobs:
   docs-build:
     name: Build

docs/cache-and-resume.md

@@ -141,7 +141,7 @@ channel.of(1,2,3).map { v -> def X=v; X+=2 }.view { v -> "ch1 = $v" }
 ```
 
 :::{versionadded} 25.04.0
-The {ref}`strict syntax <strict-syntax-page>` does not allow global variables to be declared in closures.
+The {ref}`strict parser <strict-syntax-page>` does not allow global variables to be declared in closures.
 :::
 
 (cache-nondeterministic-inputs)=

docs/config.md

@@ -320,7 +320,7 @@ nextflow run main.nf -profile standard,cloud
 Nextflow applies config profiles in the order in which they were defined in the config, regardless of the order you specify them on the command line.
 
 :::{versionadded} 25.04.0
-When using the {ref}`strict syntax <strict-syntax-page>`, Nextflow applies profiles in the order you specify them on the command line.
+When using the {ref}`strict parser <strict-syntax-page>`, Nextflow applies profiles in the order you specify them on the command line.
 :::
 
 (config-workflow-handlers)=

docs/migrations/25-04.md

@@ -8,13 +8,13 @@
 
 <h3>Strict syntax</h3>
 
-The *strict syntax* is a strict parser for Nextflow DSL2 that implements the {ref}`Nextflow language specification <syntax-page>`. Originally introduced by the [Nextflow language server](https://github.com/nextflow-io/language-server) alongside Nextflow 24.10, the strict syntax is now available in the Nextflow CLI.
+The *strict syntax parser* is a strict implementation of Nextflow DSL2 based on the {ref}`Nextflow language specification <syntax-page>`. Originally introduced by the [Nextflow language server](https://github.com/nextflow-io/language-server) alongside Nextflow 24.10, the strict parser is now available in the Nextflow CLI.
 
-The strict syntax is disabled by default. Enable it by setting the environment variable `NXF_SYNTAX_PARSER=v2`. See {ref}`strict-syntax-page` for details.
+The strict parser is disabled by default. Enable it by setting the environment variable `NXF_SYNTAX_PARSER=v2`. See {ref}`strict-syntax-page` for details.
 
 <h3>Linting and formatting</h3>
 
-The `nextflow lint` command checks Nextflow scripts and config files for errors using the {ref}`strict syntax <strict-syntax-page>`. It can also format Nextflow files using the same formatter as the Nextflow language server. See {ref}`cli-lint` for details.
+The `nextflow lint` command checks Nextflow scripts and config files for errors using the {ref}`strict parser <strict-syntax-page>`. It can also format Nextflow files using the same formatter as the Nextflow language server. See {ref}`cli-lint` for details.
 
 (workflow-outputs-third-preview)=
 

docs/migrations/25-10.md

@@ -9,7 +9,7 @@
 <h3>Workflow params</h3>
 
 :::{note}
-Typed parameters require the {ref}`strict syntax <strict-syntax-page>`. Set the `NXF_SYNTAX_PARSER` environment variable to `v2` to enable:
+Typed parameters require the {ref}`strict parser <strict-syntax-page>`. Set the `NXF_SYNTAX_PARSER` environment variable to `v2` to enable:
 
 ```bash
 export NXF_SYNTAX_PARSER=v2
@@ -73,7 +73,7 @@ See {ref}`migrating-workflow-outputs` to get started.
 <h3>Static typing (preview)</h3>
 
 :::{note}
-Static typing requires the {ref}`strict syntax <strict-syntax-page>`. Set the `NXF_SYNTAX_PARSER` environment variable to `v2` to enable:
+Static typing requires the {ref}`strict parser <strict-syntax-page>`. Set the `NXF_SYNTAX_PARSER` environment variable to `v2` to enable:
 
 ```bash
 export NXF_SYNTAX_PARSER=v2
@@ -209,7 +209,7 @@ Plugins should be updated to publish to the Nextflow plugin registry using the {
 <h3>New syntax for workflow handlers</h3>
 
 :::{note}
-The new syntax for workflow handlers require the {ref}`strict syntax <strict-syntax-page>`. Set the `NXF_SYNTAX_PARSER` environment variable to `v2` to enable:
+The new syntax for workflow handlers requires the {ref}`strict parser <strict-syntax-page>`. Set the `NXF_SYNTAX_PARSER` environment variable to `v2` to enable:
 
 ```bash
 export NXF_SYNTAX_PARSER=v2
@@ -231,11 +231,11 @@ workflow {
 }
 ```
 
-This syntax is simpler and easier to use with the {ref}`strict syntax <strict-syntax-page>`. See {ref}`workflow-handlers` for details.
+This syntax is simpler and easier to use with the {ref}`strict parser <strict-syntax-page>`. See {ref}`workflow-handlers` for details.
 
 <h3>Simpler syntax for dynamic directives</h3>
 
-The {ref}`strict syntax <strict-syntax-page>` allows dynamic process directives to be specified without a closure:
+The {ref}`strict parser <strict-syntax-page>` allows dynamic process directives to be specified without a closure:
 
 ```nextflow
 process hello {
@@ -284,11 +284,11 @@ This feature addresses previous inconsistencies in timestamp representations.
 
 ## Deprecations
 
-- The legacy type detection of CLI parameters is disabled when using the strict syntax (`NXF_SYNTAX_PARSER=v2`). {ref}`Legacy parameters <workflow-params-legacy>` in the strict syntax should not rely on legacy type detection. Alternatively, use the new `params` block to convert CLI parameters based on their type annotations. Legacy type detection can be disabled globally by setting the environment variable `NXF_DISABLE_PARAMS_TYPE_DETECTION=true`.
+- The legacy type detection of CLI parameters is disabled when using the strict parser (`NXF_SYNTAX_PARSER=v2`). {ref}`Legacy parameters <workflow-params-legacy>` should not rely on legacy type detection. Alternatively, use the new `params` block to convert CLI parameters based on their type annotations. Legacy type detection can be disabled globally by setting the environment variable `NXF_DISABLE_PARAMS_TYPE_DETECTION=true`.
 
 - The use of workflow handlers in the configuration file has been deprecated. You should define workflow handlers in the pipeline script or a plugin instead. See {ref}`config-workflow-handlers` for details.
 
-- The `nextflow.enable.configProcessNamesValidation` feature flag is deprecated. It was originally introduced to suppress false warnings for process selectors targeting conditional processes. The {ref}`strict syntax <strict-syntax-page>` now validates process selectors without producing false warnings.
+- The `nextflow.enable.configProcessNamesValidation` feature flag is deprecated. It was originally introduced to suppress false warnings for process selectors targeting conditional processes. The {ref}`strict parser <strict-syntax-page>` now validates process selectors without producing false warnings.
 
 ## Miscellaneous
 

docs/migrations/26-04.md

@@ -382,7 +382,7 @@ A Platform access token with appropriate permissions is required to download non
 
 ## Deprecations
 
-- The `nextflow.enable.strict` feature flag is deprecated. It is not needed when {ref}`strict syntax <strict-syntax-page>` is enabled.
+- The `nextflow.enable.strict` feature flag is deprecated. It is not needed when usiung the {ref}`strict parser <strict-syntax-page>`.
 
 - The `manifest.defaultBranch` config option is deprecated. Nextflow can automatically detect the default branch when using a remote pipeline.
 

docs/process-typed.md

@@ -30,7 +30,7 @@ process hello {
 
 To use this feature:
 
-1. Enable the {ref}`strict syntax <strict-syntax-page>` by setting the `NXF_SYNTAX_PARSER` environment variable to `v2`:
+1. Enable the {ref}`strict parser <strict-syntax-page>` by setting the `NXF_SYNTAX_PARSER` environment variable to `v2`:
 
     ```bash
     export NXF_SYNTAX_PARSER=v2

docs/process.md

@@ -211,8 +211,8 @@ Template scripts are generally discouraged due to the caveats described above. T
 
 ### Shell
 
-:::{deprecated} 24.11.0-edge
-Use the `script` section instead. Consider using the {ref}`strict syntax <strict-syntax-page>`, which provides error checking to help distinguish between Nextflow variables and Bash variables in the process script.
+:::{deprecated} 25.04.0
+Use the `script` section instead.
 :::
 
 The `shell` section is a string expression that defines the script that is executed by the process. It is an alternative to the {ref}`process-script` definition with one important difference: it uses the exclamation mark `!` character, instead of the usual dollar `$` character, to denote Nextflow variables.
@@ -1036,8 +1036,7 @@ The `tuple` qualifier outputs multiple values in a single output as a {ref}`tupl
 ```nextflow
 process blast {
   input:
-    val species
-    path query
+    tuple val(species), path(query)
 
   output:
     tuple val(species), path('result')
@@ -1052,7 +1051,7 @@ workflow {
   ch_species = channel.of('human', 'cow', 'horse')
   ch_query = channel.fromPath('*.fa')
 
-  blast(ch_species, ch_query)
+  blast(ch_species.combine(ch_query))
 }
 ```
 
@@ -1257,7 +1256,7 @@ All directives can be assigned a dynamic value except the following:
 :::{versionadded} 25.10
 :::
 
-Dynamic directives can be specified without a closure when using the {ref}`strict syntax <strict-syntax-page>`:
+Dynamic directives can be specified without a closure when using the {ref}`strict parser <strict-syntax-page>`:
 
 ```nextflow
 queue (entries > 100 ? 'long' : 'short')

docs/reference/env-vars.md

@@ -238,9 +238,13 @@ The following environment variables control the configuration of the Nextflow ru
 : Enable the use of Spack recipes defined by using the {ref}`process-spack` directive. (default: `false`).
 
 `NXF_SYNTAX_PARSER`
-: :::{versionadded} 25.02.0-edge
+: :::{versionadded} 25.04.0
+  The strict parser is disabled by default.
+  :::
+: :::{versionchanged} 26.04.0
+  The strict parser is enabled by default.
   :::
-: Set to `'v2'` to use the {ref}`strict syntax <strict-syntax-page>` for Nextflow scripts and config files (default: `'v1'`).
+: Set to `'v2'` to use the {ref}`strict syntax parser <strict-syntax-page>` for Nextflow code. Set to `'v1'` to fall back to the legacy parser.
 
 `NXF_TEMP`
 : Directory where temporary files are stored