Merge branch 'master' into data-lineage-simplify-fragment

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

docs/cache-and-resume.md

@@ -113,8 +113,8 @@ While Nextflow tries to make it easy to write safe concurrent code, it is still
 Consider the following example:
 
 ```nextflow
-Channel.of(1,2,3) | map { v -> X=v; X+=2 } | view { v -> "ch1 = $v" }
-Channel.of(1,2,3) | map { v -> X=v; X*=2 } | view { v -> "ch2 = $v" }
+channel.of(1,2,3) | map { v -> X=v; X+=2 } | view { v -> "ch1 = $v" }
+channel.of(1,2,3) | map { v -> X=v; X*=2 } | view { v -> "ch2 = $v" }
 ```
 
 The problem here is that `X` is declared in each `map` closure without the `def` keyword (or other type qualifier). Using the `def` keyword makes the variable local to the enclosing scope; omitting the `def` keyword makes the variable global to the entire script.
@@ -125,10 +125,10 @@ The solution is to not use a global variable where a local variable is enough (o
 
 ```nextflow
 // local variable
-Channel.of(1,2,3) | map { v -> def X=v; X+=2 } | view { v -> "ch1 = $v" }
+channel.of(1,2,3) | map { v -> def X=v; X+=2 } | view { v -> "ch1 = $v" }
 
 // no variable
-Channel.of(1,2,3) | map { v -> v * 2 } | view { v -> "ch2 = $v" }
+channel.of(1,2,3) | map { v -> v * 2 } | view { v -> "ch2 = $v" }
 ```
 
 (cache-nondeterministic-inputs)=
@@ -139,8 +139,8 @@ Sometimes a process needs to merge inputs from different sources. Consider the f
 
 ```nextflow
 workflow {
-    ch_foo = Channel.of( ['1', '1.foo'], ['2', '2.foo'] )
-    ch_bar = Channel.of( ['2', '2.bar'], ['1', '1.bar'] )
+    ch_foo = channel.of( ['1', '1.foo'], ['2', '2.foo'] )
+    ch_bar = channel.of( ['2', '2.bar'], ['1', '1.bar'] )
     gather(ch_foo, ch_bar)
 }
 
@@ -162,8 +162,8 @@ The solution is to explicitly join the two channels before the process invocatio
 
 ```nextflow
 workflow {
-    ch_foo = Channel.of( ['1', '1.foo'], ['2', '2.foo'] )
-    ch_bar = Channel.of( ['2', '2.bar'], ['1', '1.bar'] )
+    ch_foo = channel.of( ['1', '1.foo'], ['2', '2.foo'] )
+    ch_bar = channel.of( ['2', '2.bar'], ['1', '1.bar'] )
     gather(ch_foo.join(ch_bar))
 }
 

docs/channel.md

@@ -66,16 +66,12 @@ See also: {ref}`process-multiple-input-channels`.
 
 Channel factories are functions that can create channels.
 
-For example, the `Channel.of()` factory can be used to create a channel from an arbitrary list of arguments:
+For example, the `channel.of()` factory can be used to create a channel from an arbitrary list of arguments:
 
 ```nextflow
-Channel.of(1, 2, 3).view()
+channel.of(1, 2, 3).view()
 ```
 
-:::{versionadded} 20.07.0
-`channel` was introduced as an alias of `Channel`, allowing factory methods to be specified as `channel.of()` or `Channel.of()`, and so on.
-:::
-
 See {ref}`channel-factory` for the full list of channel factories.
 
 ## Operators

docs/flux.md

@@ -38,7 +38,7 @@ Here is an example pipeline that we will use:
 
 ```nextflow
 workflow {
-    breakfast = Channel.of '🥞️', '🥑️', '🥧️', '🍵️', '🍞️'
+    breakfast = channel.of '🥞️', '🥑️', '🥧️', '🍵️', '🍞️'
     haveMeal(breakfast)
 }
 

docs/migrations/25-04.md

@@ -37,6 +37,10 @@ The third preview of workflow outputs introduces the following breaking changes
 
 See {ref}`workflow-output-def` to learn more about the workflow output definition.
 
+<h3>Topic channels (out of preview)</h3>
+
+{ref}`Topic channels <channel-topic>`, introduced in Nextflow 24.04 as a preview feature, have been brought out of preview, which means that they can be used without the `nextflow.preview.topic` feature flag.
+
 <h3>Data lineage</h3>
 
 This release introduces built-in provenance tracking, also known as *data lineage*. When `lineage.enabled` is set to `true` in your configuration, Nextflow will record every workflow run, task execution, output file, and the links between them.

docs/migrations/dsl1.md

@@ -152,6 +152,7 @@ DSL2 scripts cannot exceed 64 KB in size. Split large DSL1 scripts into modules
 
 <h3>Channels</h3>
 
+- Channel factories should be accessed through the `channel` namespace instead of the `Channel` type, although they can still be accessed through either method.
 - Channel method `bind` has been deprecated in DSL2.
 - Channel method `<<` has been deprecated in DSL2.
 - Channel factory `create` has been deprecated in DSL2.

docs/overview.md

@@ -55,7 +55,7 @@ process extractTopHits {
 }
 
 workflow {
-  def query_ch = Channel.fromPath(params.query)
+  def query_ch = channel.fromPath(params.query)
   blastSearch(query_ch, params.db)
   extractTopHits(blastSearch.out, params.db).view()
 }

docs/process.md

@@ -171,7 +171,7 @@ process templateExample {
 }
 
 workflow {
-    Channel.of('this', 'that') | templateExample
+    channel.of('this', 'that') | templateExample
 }
 ```
 
@@ -228,7 +228,7 @@ process myTask {
 }
 
 workflow {
-    Channel.of('Hello', 'Hola', 'Bonjour') | myTask
+    channel.of('Hello', 'Hola', 'Bonjour') | myTask
 }
 ```
 
@@ -258,7 +258,7 @@ process simpleSum {
 }
 
 workflow {
-    Channel.of('a', 'b', 'c') | simpleSum
+    channel.of('a', 'b', 'c') | simpleSum
 }
 ```
 
@@ -352,7 +352,7 @@ process basicExample {
 }
 
 workflow {
-  def num = Channel.of(1,2,3)
+  def num = channel.of(1,2,3)
   basicExample(num)
 }
 ```
@@ -384,7 +384,7 @@ process basicExample {
 }
 
 workflow {
-  Channel.of(1,2,3) | basicExample
+  channel.of(1,2,3) | basicExample
 }
 ```
 :::
@@ -407,7 +407,7 @@ process blastThemAll {
 }
 
 workflow {
-  def proteins = Channel.fromPath( '/some/path/*.fa' )
+  def proteins = channel.fromPath( '/some/path/*.fa' )
   blastThemAll(proteins)
 }
 ```
@@ -444,7 +444,7 @@ process blastThemAll {
 }
 
 workflow {
-  def proteins = Channel.fromPath( '/some/path/*.fa' )
+  def proteins = channel.fromPath( '/some/path/*.fa' )
   blastThemAll(proteins)
 }
 ```
@@ -455,7 +455,7 @@ In this example, each file received by the process is staged with the name `quer
 This feature allows you to execute the process command multiple times without worrying about the file names changing. In other words, Nextflow helps you write pipeline tasks that are self-contained and decoupled from the execution environment. As a best practice, you should avoid referencing files in your process script other than those defined in your input block.
 :::
 
-Channel factories like `Channel.fromPath` produce file objects, but a `path` input can also accept a string literal path. The string value should be an absolute path, i.e. it must be prefixed with a `/` character or a supported URI protocol (`file://`, `http://`, `s3://`, etc), and it cannot contain special characters (`\n`, etc).
+Channel factories like `channel.fromPath` produce file objects, but a `path` input can also accept a string literal path. The string value should be an absolute path, i.e. it must be prefixed with a `/` character or a supported URI protocol (`file://`, `http://`, `s3://`, etc), and it cannot contain special characters (`\n`, etc).
 
 ```nextflow
 process foo {
@@ -501,7 +501,7 @@ process blastThemAll {
 }
 
 workflow {
-    def fasta = Channel.fromPath( "/some/path/*.fa" ).buffer(size: 3)
+    def fasta = channel.fromPath( "/some/path/*.fa" ).buffer(size: 3)
     blastThemAll(fasta)
 }
 ```
@@ -543,7 +543,7 @@ process blastThemAll {
 }
 
 workflow {
-    def fasta = Channel.fromPath( "/some/path/*.fa" ).buffer(size: 3)
+    def fasta = channel.fromPath( "/some/path/*.fa" ).buffer(size: 3)
     blastThemAll(fasta)
 }
 ```
@@ -609,7 +609,7 @@ process printEnv {
 }
 
 workflow {
-    Channel.of('hello', 'hola', 'bonjour', 'ciao') | printEnv
+    channel.of('hello', 'hola', 'bonjour', 'ciao') | printEnv
 }
 ```
 
@@ -636,7 +636,7 @@ process printAll {
 }
 
 workflow {
-  Channel.of('hello', 'hola', 'bonjour', 'ciao')
+  channel.of('hello', 'hola', 'bonjour', 'ciao')
     | map { v -> v + '\n' }
     | printAll
 }
@@ -670,7 +670,7 @@ process tupleExample {
 }
 
 workflow {
-  Channel.of( [1, 'alpha.txt'], [2, 'beta.txt'], [3, 'delta.txt'] ) | tupleExample
+  channel.of( [1, 'alpha.txt'], [2, 'beta.txt'], [3, 'delta.txt'] ) | tupleExample
 }
 ```
 
@@ -695,7 +695,7 @@ process alignSequences {
 }
 
 workflow {
-  sequences = Channel.fromPath('*.fa')
+  sequences = channel.fromPath('*.fa')
   methods = ['regular', 'espresso', 'psicoffee']
 
   alignSequences(sequences, methods)
@@ -720,7 +720,7 @@ process alignSequences {
 }
 
 workflow {
-  sequences = Channel.fromPath('*.fa')
+  sequences = channel.fromPath('*.fa')
   methods = ['regular', 'espresso']
   libraries = [ file('PQ001.lib'), file('PQ002.lib'), file('PQ003.lib') ]
 
@@ -763,8 +763,8 @@ process foo {
 }
 
 workflow {
-  x = Channel.of(1, 2)
-  y = Channel.of('a', 'b', 'c')
+  x = channel.of(1, 2)
+  y = channel.of('a', 'b', 'c')
   foo(x, y)
 }
 ```
@@ -776,7 +776,7 @@ The process `foo` is executed two times because the `x` channel emits only two v
 2 and b
 ```
 
-A different semantic is applied when using a {ref}`value channel <channel-type-value>`. This kind of channel is created by the {ref}`Channel.value <channel-value>` factory method or implicitly when a process is invoked with an argument that is not a channel. By definition, a value channel is bound to a single value and it can be read an unlimited number of times without consuming its content. Therefore, when mixing a value channel with one or more (queue) channels, it does not affect the process termination because the underlying value is applied repeatedly.
+A different semantic is applied when using a {ref}`value channel <channel-type-value>`. This kind of channel is created by the {ref}`channel.value <channel-value>` factory method or implicitly when a process is invoked with an argument that is not a channel. By definition, a value channel is bound to a single value and it can be read an unlimited number of times without consuming its content. Therefore, when mixing a value channel with one or more (queue) channels, it does not affect the process termination because the underlying value is applied repeatedly.
 
 To better understand this behavior, compare the previous example with the following one:
 
@@ -793,8 +793,8 @@ process bar {
 }
 
 workflow {
-  x = Channel.value(1)
-  y = Channel.of('a', 'b', 'c')
+  x = channel.value(1)
+  y = channel.of('a', 'b', 'c')
   foo(x, y)
 }
 ```
@@ -887,7 +887,7 @@ process foo {
 }
 
 workflow {
-  ch_dummy = Channel.fromPath('*').first()
+  ch_dummy = channel.fromPath('*').first()
   (ch_var, ch_str, ch_exp) = foo(ch_dummy)
 
   ch_var.view { var -> "ch_var: $var" }
@@ -1074,8 +1074,8 @@ process blast {
 }
 
 workflow {
-  ch_species = Channel.of('human', 'cow', 'horse')
-  ch_query = Channel.fromPath('*.fa')
+  ch_species = channel.of('human', 'cow', 'horse')
+  ch_query = channel.fromPath('*.fa')
 
   blast(ch_species, ch_query)
 }

docs/reference/channel.md

@@ -362,7 +362,7 @@ Available retry policy properties:
 | `maxAttempts` | Max attempts when retrying failed SRA requests. | `3`     |
 | `maxDelay`    | Max delay when retrying failed SRA requests.    | `30s`   |
 
-The following code snippet shows an example for using the `Channel.fromSRA` factory method with a custom `retryPolicy`.
+The following code snippet shows an example for using the `channel.fromSRA` factory method with a custom `retryPolicy`.
 
   ```nextflow
   channel.fromSRA(ids, retryPolicy: [delay: '250ms', maxAttempts: 5])
@@ -375,16 +375,16 @@ The following code snippet shows an example for using the `Channel.fromSRA` fact
 The `interval` method emits an incrementing index (starting from zero) at a periodic interval. For example:
 
 ```nextflow
-Channel.interval('1s').view()
+channel.interval('1s').view()
 ```
 
 The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as {ref}`operator-take` or {ref}`operator-until` to close the channel based on a stopping condition.
 
-An optional closure can be used to transform the index. Additionally, returning `Channel.STOP` will close the channel. For example:
+An optional closure can be used to transform the index. Additionally, returning `channel.STOP` will close the channel. For example:
 
 ```nextflow
-ch = Channel.interval('1s') { i ->
-    i == 10 ? Channel.STOP : i
+ch = channel.interval('1s') { i ->
+    i == 10 ? channel.STOP : i
 }
 ch.view()
 ```
@@ -444,7 +444,7 @@ See also: [channel.fromList](#fromlist) factory method.
 :::
 
 :::{note}
-This feature requires the `nextflow.preview.topic` feature flag to be enabled.
+In versions of Nextflow prior to 25.04, this feature requires the `nextflow.preview.topic` feature flag to be enabled.
 :::
 
 A *topic channel* is a queue channel that can receive values from many source channels *implicitly* based on a matching *topic name*.

docs/reference/cli.md

@@ -1376,7 +1376,7 @@ process sayHello {
 }
 
 workflow {
-  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+  channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
 }
 ```
 
@@ -1416,6 +1416,6 @@ process sayHello {
 }
 
 workflow {
-  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+  channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
 }
 ```

docs/reference/feature-flags.md

@@ -61,5 +61,7 @@ Feature flags are used to introduce experimental or other opt-in features. They
 `nextflow.preview.topic`
 : :::{versionadded} 23.11.0-edge
   :::
-: *Experimental: may change in a future release.*
+: :::{versionchanged} 25.04.0
+  This feature flag is no longer required to use topic channels.
+  :::
 : When `true`, enables {ref}`topic channels <channel-topic>` feature.

docs/reference/operator.md

@@ -1041,13 +1041,13 @@ By default, the first item is used as the initial accumulated value. You can opt
 The `set` operator assigns a source channel to a variable, whose name is specified as a closure parameter:
 
 ```nextflow
-Channel.of(10, 20, 30).set { my_channel }
+channel.of(10, 20, 30).set { my_channel }
 ```
 
 Using `set` is semantically equivalent to assigning a variable:
 
 ```nextflow
-my_channel = Channel.of(10, 20, 30)
+my_channel = channel.of(10, 20, 30)
 ```
 
 See also: [tap](#tap)
@@ -1236,7 +1236,7 @@ Channel
 ```
 
 :::{note}
-`Channel.fromFilePairs()` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
+`channel.fromFilePairs()` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
 :::
 
 :::{note}

docs/reference/process.md

@@ -1624,7 +1624,7 @@ process foo {
 }
 
 workflow {
-  Channel.of('alpha', 'gamma', 'omega') | foo
+  channel.of('alpha', 'gamma', 'omega') | foo
 }
 ```
 

docs/reference/stdlib-namespaces.md

@@ -79,7 +79,7 @@ The global namespace contains globally available constants and functions.
   `type: String`
   : Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`)
 
-: See also: {ref}`Channel.fromPath <channel-path>`.
+: See also: {ref}`channel.fromPath <channel-path>`.
 
 `files( filePattern: String, [options] ) -> List<Path>`
 : Get a collection of files from a file name or glob pattern. Supports the same options as `file()`.