Merge pull request #235 from nextflow-io/update-to-23.04.1

Update Nextflow version to 23.04.1

docs/basic_training/channels.md

@@ -85,33 +85,9 @@ When you run the script, it prints only 2, as you can see below:
 2
 ```
 
-To understand why, we can inspect the queue channel and running Nextflow with DSL1 gives us a more explicit comprehension of what is behind the curtains.
+A process will only instantiate a task when there are elements to be consumed from _all_ the channels provided as input to it. Because `ch1` and `ch2` are queue channels, and the single element of `ch2` has been consumed, no new process instances will be launched, even if there are other elements to be consumed in `ch1`.
 
-```groovy linenums="1"
-ch1 = Channel.of(1)
-println ch1
-```
-
-```console
-$ nextflow run example.nf -dsl1
-...
-DataflowQueue(queue=[DataflowVariable(value=1), DataflowVariable(value=groovyx.gpars.dataflow.operator.PoisonPill@34be065a)])
-```
-
-We have the value 1 as the single element of our queue channel and a poison pill, which will tell the process that there’s nothing left to be consumed. That’s why we only have one output for the example above, which is 2. Let’s inspect a value channel now.
-
-```groovy linenums="1"
-ch1 = Channel.value(1)
-println ch1
-```
-
-```console
-$ nextflow run example.nf -dsl1
-...
-DataflowVariable(value=1)
-```
-
-There is no poison pill, and that’s why we get a different output with the code below, where `ch2` is turned into a value channel through the `first` operator.
+To use the single element in `ch2` multiple times, we can either use `Channel.value` as mentioned above, or use a channel operator that returns a single element such as `first()` below:
 
 ```groovy linenums="1"
 ch1 = Channel.of(1, 2, 3)

docs/basic_training/channels.pt.md

@@ -85,29 +85,37 @@ Ao rodar o script, ele imprime apenas 2, como você pode ver abaixo:
 2
 ```
 
-Para entender o motivo, podemos inspecionar o canal de fila executando o Nextflow com DSL1, o que nos dá uma compreensão mais explícita do que está por trás das cortinas.
+Para entender o motivo, podemos inspecionar o canal de fila executando o Nextflow com DSL1, o que nos dá uma compreensão mais explícita do que está por trás das cortinas. Salve o script abaixo como `exemplo2.nf`.
 
-```groovy linenums="1"
+```groovy linenums="1" title="exemplo2.nf"
 canal1 = Channel.of(1)
 println canal1
 ```
 
 ```console
-$ nextflow run exemplo.nf -dsl1
-...
-DataflowQueue(queue=[DataflowVariable(value=1), DataflowVariable(value=groovyx.gpars.dataflow.operator.PoisonPill@34be065a)])
+$ NXF_VER=22.10.4 nextflow run exemplo2.nf -dsl1
+```
+
+Output:
+
+```console
+DataflowQueue(queue=[DataflowVariable(value=1), DataflowVariable(value=groovyx.gpars.dataflow.operator.PoisonPill@ed2f2f6)])
 ```
 
 Temos o valor 1 como único elemento do nosso canal de fila e uma pílula de veneno, que vai dizer ao processo que não há mais nada para ser consumido. É por isso que temos apenas uma saída para o exemplo acima, que é 2. Vamos inspecionar um canal de valor agora.
 
-```groovy linenums="1"
+```groovy linenums="1" title="exemplo3.nf"
 canal1 = Channel.value(1)
 println canal1
 ```
 
 ```console
-$ nextflow run exemplo.nf -dsl1
-...
+$ NXF_VER=22.10.4 nextflow run exemplo3.nf -dsl1
+```
+
+Output:
+
+```console
 DataflowVariable(value=1)
 ```
 

docs/basic_training/intro.fr.md

@@ -161,11 +161,11 @@ nextflow run hello.nf
 Le résultat ressemblera au texte ci-dessous :
 
 ```linenums="1"
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [gigantic_poitras] DSL2 - revision: 197a0e289a
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [cheeky_keller] DSL2 - revision: 197a0e289a
 executor >  local (3)
-[c8/c36893] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
-[1a/3c54ed] process > CONVERTTOUPPER (2) [100%] 2 of 2 ✔
+[31/52c31e] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
+[37/b9332f] process > CONVERTTOUPPER (2) [100%] 2 of 2 ✔
 HELLO
 WORLD!
 ```
@@ -181,11 +181,11 @@ La sortie standard affiche (ligne par ligne) :
 
 !!! info
 
-    Les nombres hexadécimaux, comme `c8/c36893`, identifient l'exécution unique du processus, que nous appelons une tâche. Ces nombres sont également le préfixe des répertoires où chaque tâche est exécutée. Vous pouvez inspecter les fichiers produits en allant dans le répertoire `$PWD/work` et en utilisant ces numéros pour trouver le chemin d'exécution spécifique à la tâche.
+    Les nombres hexadécimaux, comme `31/52c31e`, identifient l'exécution unique du processus, que nous appelons une tâche. Ces nombres sont également le préfixe des répertoires où chaque tâche est exécutée. Vous pouvez inspecter les fichiers produits en allant dans le répertoire `$PWD/work` et en utilisant ces numéros pour trouver le chemin d'exécution spécifique à la tâche.
 
 !!! tip
 
-    Le second processus s'exécute deux fois, dans deux répertoires de travail différents pour chaque fichier d'entrée. La sortie du journal [ANSI](https://en.wikipedia.org/wiki/ANSI_escape_code) de Nextflow se rafraîchit dynamiquement au fur et à mesure que le workflow s'exécute ; dans l'exemple précédent, le répertoire de travail `[1a/3c54ed]` est le second des deux répertoires qui ont été traités (en écrasant le journal avec le premier). Pour imprimer tous les chemins pertinents à l'écran, désactivez la sortie du journal ANSI en utilisant l'option `-ansi-log` (par exemple, `nextflow run hello.nf -ansi-log false`).
+    Le second processus s'exécute deux fois, dans deux répertoires de travail différents pour chaque fichier d'entrée. La sortie du journal [ANSI](https://en.wikipedia.org/wiki/ANSI_escape_code) de Nextflow se rafraîchit dynamiquement au fur et à mesure que le workflow s'exécute ; dans l'exemple précédent, le répertoire de travail `[37/b9332f]` est le second des deux répertoires qui ont été traités (en écrasant le journal avec le premier). Pour imprimer tous les chemins pertinents à l'écran, désactivez la sortie du journal ANSI en utilisant l'option `-ansi-log` (par exemple, `nextflow run hello.nf -ansi-log false`).
 
 Il faut noter que le processus `CONVERTTOUPPER` est exécuté en parallèle, donc il n'y a aucune garantie que l'instance qui traite le premier split (le chunk _Hello ') sera exécutée avant celle qui traite le second split (le chunk 'world!_).
 
@@ -224,11 +224,11 @@ Enregistrez ensuite le fichier sous le même nom et exécutez-le en ajoutant l'o
 ```console
 $ nextflow run hello.nf -resume
 
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [amazing_becquerel] DSL2 - revision: 525206806b
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [zen_colden] DSL2 - revision: 0676c711e8
 executor >  local (2)
-[c8/c36893] process > SPLITLETTERS (1)   [100%] 1 of 1, cached: 1 ✔
-[77/cf83b6] process > CONVERTTOUPPER (1) [100%] 2 of 2 ✔
+[31/52c31e] process > SPLITLETTERS (1)   [100%] 1 of 1, cached: 1 ✔
+[0f/8175a7] process > CONVERTTOUPPER (1) [100%] 2 of 2 ✔
 !dlrow
  olleH
 ```
@@ -252,14 +252,14 @@ nextflow run hello.nf --greeting 'Bonjour le monde!'
 La chaîne spécifiée sur la ligne de commande remplacera la valeur par défaut du paramètre. La sortie ressemblera à ceci :
 
 ```
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [fervent_galileo] DSL2 - revision: 525206806b
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [goofy_kare] DSL2 - revision: 0676c711e8
 executor >  local (4)
-[e9/139d7d] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
-[bb/fc8548] process > CONVERTTOUPPER (1) [100%] 3 of 3 ✔
+[8b/7c7d13] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
+[58/3b2df0] process > CONVERTTOUPPER (3) [100%] 3 of 3 ✔
+uojnoB
 m el r
 !edno
-uojnoB
 ```
 
 ### Au format DAG

docs/basic_training/intro.md

@@ -161,11 +161,11 @@ nextflow run hello.nf
 The output will look similar to the text shown below:
 
 ```linenums="1"
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [gigantic_poitras] DSL2 - revision: 197a0e289a
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [cheeky_keller] DSL2 - revision: 197a0e289a
 executor >  local (3)
-[c8/c36893] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
-[1a/3c54ed] process > CONVERTTOUPPER (2) [100%] 2 of 2 ✔
+[31/52c31e] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
+[37/b9332f] process > CONVERTTOUPPER (2) [100%] 2 of 2 ✔
 HELLO
 WORLD!
 ```
@@ -181,11 +181,11 @@ The standard output shows (line by line):
 
 !!! info
 
-    The hexadecimal numbers, like `c8/c36893`, identify the unique process execution, that we call a task. These numbers are also the prefix of the directories where each task is executed. You can inspect the files produced by changing to the directory `$PWD/work` and using these numbers to find the task-specific execution path.
+    The hexadecimal numbers, like `31/52c31e`, identify the unique process execution, that we call a task. These numbers are also the prefix of the directories where each task is executed. You can inspect the files produced by changing to the directory `$PWD/work` and using these numbers to find the task-specific execution path.
 
 !!! tip
 
-    The second process runs twice, executing in two different work directories for each input file. The [ANSI](https://en.wikipedia.org/wiki/ANSI_escape_code) log output from Nextflow dynamically refreshes as the workflow runs; in the previous example the work directory `[1a/3c54ed]` is the second of the two directories that were processed (overwriting the log with the first). To print all the relevant paths to the screen, disable the ANSI log output using the `-ansi-log` flag (e.g., `nextflow run hello.nf -ansi-log false`).
+    The second process runs twice, executing in two different work directories for each input file. The [ANSI](https://en.wikipedia.org/wiki/ANSI_escape_code) log output from Nextflow dynamically refreshes as the workflow runs; in the previous example the work directory `[37/b9332f]` is the second of the two directories that were processed (overwriting the log with the first). To print all the relevant paths to the screen, disable the ANSI log output using the `-ansi-log` flag (e.g., `nextflow run hello.nf -ansi-log false`).
 
 It’s worth noting that the process `CONVERTTOUPPER` is executed in parallel, so there’s no guarantee that the instance processing the first split (the chunk _Hello ') will be executed before the one processing the second split (the chunk 'world!_).
 
@@ -224,11 +224,11 @@ Then save the file with the same name, and execute it by adding the `-resume` op
 ```console
 $ nextflow run hello.nf -resume
 
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [amazing_becquerel] DSL2 - revision: 525206806b
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [zen_colden] DSL2 - revision: 0676c711e8
 executor >  local (2)
-[c8/c36893] process > SPLITLETTERS (1)   [100%] 1 of 1, cached: 1 ✔
-[77/cf83b6] process > CONVERTTOUPPER (1) [100%] 2 of 2 ✔
+[31/52c31e] process > SPLITLETTERS (1)   [100%] 1 of 1, cached: 1 ✔
+[0f/8175a7] process > CONVERTTOUPPER (1) [100%] 2 of 2 ✔
 !dlrow
  olleH
 ```
@@ -252,14 +252,14 @@ nextflow run hello.nf --greeting 'Bonjour le monde!'
 The string specified on the command line will override the default value of the parameter. The output will look like this:
 
 ```
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [fervent_galileo] DSL2 - revision: 525206806b
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [goofy_kare] DSL2 - revision: 0676c711e8
 executor >  local (4)
-[e9/139d7d] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
-[bb/fc8548] process > CONVERTTOUPPER (1) [100%] 3 of 3 ✔
+[8b/7c7d13] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
+[58/3b2df0] process > CONVERTTOUPPER (3) [100%] 3 of 3 ✔
+uojnoB
 m el r
 !edno
-uojnoB
 ```
 
 ### In DAG-like format

docs/basic_training/intro.pt.md

@@ -160,11 +160,11 @@ nextflow run hello.nf
 A saída será semelhante ao texto mostrado abaixo:
 
 ```linenums="1"
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [gigantic_poitras] DSL2 - revision: 197a0e289a
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [cheeky_keller] DSL2 - revision: 197a0e289a
 executor >  local (3)
-[c8/c36893] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
-[1a/3c54ed] process > CONVERTTOUPPER (2) [100%] 2 of 2 ✔
+[31/52c31e] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
+[37/b9332f] process > CONVERTTOUPPER (2) [100%] 2 of 2 ✔
 HELLO
 WORLD!
 ```
@@ -180,11 +180,11 @@ A saída padrão mostra (linha por linha):
 
 !!! info
 
-    Os números hexadecimais, como `c8/c36893`, identificam de forma única a execução do processo. Esses números também são o prefixo dos diretórios onde cada tarefa é executado. Você pode inspecionar os arquivos produzidos mudando para o diretório `$PWD/work` e usando esses números para encontrar o caminho de execução específico da tarefa.
+    Os números hexadecimais, como `31/52c31e`, identificam de forma única a execução do processo. Esses números também são o prefixo dos diretórios onde cada tarefa é executado. Você pode inspecionar os arquivos produzidos mudando para o diretório `$PWD/work` e usando esses números para encontrar o caminho de execução específico da tarefa.
 
 !!! tip
 
-    O segundo processo é executado duas vezes, em dois diretórios de trabalho diferentes para cada arquivo de entrada. A saída de log [ANSI](https://en.wikipedia.org/wiki/ANSI_escape_code) do Nextflow é atualizada dinamicamente conforme o fluxo de trabalho é executado; no exemplo anterior, o diretório de trabalho `[1a/3c54ed]` é o segundo dos dois diretórios que foram processados (sobrescrevendo o log com o primeiro). Para imprimir para a tela todos os caminhos relevantes, desative a saída de log ANSI usando o sinalizador `-ansi-log` (por exemplo, `nextflow run hello.nf -ansi-log false`).
+    O segundo processo é executado duas vezes, em dois diretórios de trabalho diferentes para cada arquivo de entrada. A saída de log [ANSI](https://en.wikipedia.org/wiki/ANSI_escape_code) do Nextflow é atualizada dinamicamente conforme o fluxo de trabalho é executado; no exemplo anterior, o diretório de trabalho `[37/b9332f]` é o segundo dos dois diretórios que foram processados (sobrescrevendo o log com o primeiro). Para imprimir para a tela todos os caminhos relevantes, desative a saída de log ANSI usando o sinalizador `-ansi-log` (por exemplo, `nextflow run hello.nf -ansi-log false`).
 
 Vale ressaltar que o processo `CONVERTTOUPPER` é executado em paralelo, portanto não há garantia de que a instância que processa a primeira divisão (o bloco _Hello_) será executada antes daquela que processa a segundo divisão (o bloco _world!_).
 
@@ -223,11 +223,11 @@ Em seguida, salve o arquivo com o mesmo nome e execute-o adicionando a opção `
 ```console
 $ nextflow run hello.nf -resume
 
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [amazing_becquerel] DSL2 - revision: 525206806b
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [zen_colden] DSL2 - revision: 0676c711e8
 executor >  local (2)
-[c8/c36893] process > SPLITLETTERS (1)   [100%] 1 of 1, cached: 1 ✔
-[77/cf83b6] process > CONVERTTOUPPER (1) [100%] 2 of 2 ✔
+[31/52c31e] process > SPLITLETTERS (1)   [100%] 1 of 1, cached: 1 ✔
+[0f/8175a7] process > CONVERTTOUPPER (1) [100%] 2 of 2 ✔
 !dlrow
  olleH
 ```
@@ -251,14 +251,14 @@ nextflow run hello.nf --greeting 'Bonjour le monde!'
 A string especificada na linha de comando substituirá o valor padrão do parâmetro. A saída ficará assim:
 
 ```
-N E X T F L O W  ~  version 22.04.5
-Launching `hello.nf` [fervent_galileo] DSL2 - revision: 525206806b
+N E X T F L O W  ~  version 23.04.1
+Launching `hello.nf` [goofy_kare] DSL2 - revision: 0676c711e8
 executor >  local (4)
-[e9/139d7d] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
-[bb/fc8548] process > CONVERTTOUPPER (1) [100%] 3 of 3 ✔
+[8b/7c7d13] process > SPLITLETTERS (1)   [100%] 1 of 1 ✔
+[58/3b2df0] process > CONVERTTOUPPER (3) [100%] 3 of 3 ✔
+uojnoB
 m el r
 !edno
-uojnoB
 ```
 
 ### Em formato de DAG

docs/basic_training/modules.md

@@ -132,17 +132,17 @@ workflow {
         The `hello.2.nf` output should look something like this:
 
         ```console title="Output"
-        N E X T F L O W  ~  version 22.04.3
-        Launching `hello.2.nf` [goofy_goldstine] DSL2 - revision: 449cf82eaf
+        N E X T F L O W  ~  version 23.04.1
+        Launching `hello.2.nf` [crazy_shirley] DSL2 - revision: 99f6b6e40e
         executor >  local (6)
-        [e1/5e6523] process > SPLITLETTERS_one (1)   [100%] 1 of 1 ✔
-        [14/b77deb] process > CONVERTTOUPPER_one (1) [100%] 2 of 2 ✔
-        [c0/115bd6] process > SPLITLETTERS_two (1)   [100%] 1 of 1 ✔
-        [09/f9072d] process > CONVERTTOUPPER_two (2) [100%] 2 of 2 ✔
+        [2b/ec0395] process > SPLITLETTERS_one (1)   [100%] 1 of 1 ✔
+        [d7/be3b77] process > CONVERTTOUPPER_one (1) [100%] 2 of 2 ✔
+        [04/9ffc05] process > SPLITLETTERS_two (1)   [100%] 1 of 1 ✔
+        [d9/91b029] process > CONVERTTOUPPER_two (2) [100%] 2 of 2 ✔
         WORLD!
         HELLO
-        WORLD!
         HELLO
+        WORLD!
         ```
 
 !!! tip

docs/basic_training/modules.pt.md

@@ -132,17 +132,17 @@ workflow {
         A saída de `hello.2.nf` deve ser semelhante a essa:
 
         ```console title="Output"
-        N E X T F L O W  ~  version 22.04.3
-        Launching `hello.2.nf` [goofy_goldstine] DSL2 - revision: 449cf82eaf
+        N E X T F L O W  ~  version 23.04.1
+        Launching `hello.2.nf` [crazy_shirley] DSL2 - revision: 99f6b6e40e
         executor >  local (6)
-        [e1/5e6523] process > SPLITLETTERS_one (1)   [100%] 1 of 1 ✔
-        [14/b77deb] process > CONVERTTOUPPER_one (1) [100%] 2 of 2 ✔
-        [c0/115bd6] process > SPLITLETTERS_two (1)   [100%] 1 of 1 ✔
-        [09/f9072d] process > CONVERTTOUPPER_two (2) [100%] 2 of 2 ✔
+        [2b/ec0395] process > SPLITLETTERS_one (1)   [100%] 1 of 1 ✔
+        [d7/be3b77] process > CONVERTTOUPPER_one (1) [100%] 2 of 2 ✔
+        [04/9ffc05] process > SPLITLETTERS_two (1)   [100%] 1 of 1 ✔
+        [d9/91b029] process > CONVERTTOUPPER_two (2) [100%] 2 of 2 ✔
         WORLD!
         HELLO
-        WORLD!
         HELLO
+        WORLD!
         ```
 
 !!! tip

docs/basic_training/setup.fr.md

@@ -162,11 +162,11 @@ Les dernières versions peuvent être consultées sur GitHub [ici](https://githu
 Si vous souhaitez utiliser une version spécifique de Nextflow, vous pouvez définir la variable `NXF_VER` comme indiqué ci-dessous :
 
 ```bash
-export NXF_VER=22.04.5
+export NXF_VER=23.04.1
 ```
 
 !!! Remarque
 
-    Cet atelier tutoriel nécessite `NXF_VER=22.04.0`, ou une version plus récente. Cette version utilise DSL2 par défaut.
+    Cet atelier tutoriel nécessite `NXF_VER=23.04.1`, ou une version plus récente. Cette version utilise DSL2 par défaut.
 
 Exécutez `nextflow -version` à nouveau pour confirmer que le changement a pris effet.

docs/basic_training/setup.md

@@ -162,11 +162,11 @@ The latest releases can be viewed on GitHub [here](https://github.com/nextflow-i
 If you want to use a specific version of Nextflow, you can set the `NXF_VER` variable as shown below:
 
 ```bash
-export NXF_VER=22.04.5
+export NXF_VER=23.04.1
 ```
 
 !!! Note
 
-    This tutorial workshop requires `NXF_VER=22.04.0`, or later. This version will use DSL2 as default.
+    This tutorial workshop requires `NXF_VER=23.04.1`, or later. This version will use DSL2 as default.
 
 Run `nextflow -version` again to confirm that the change has taken effect.

docs/basic_training/setup.pt.md

@@ -162,11 +162,11 @@ Os últimos lançamentos podem ser vistos no GitHub [aqui](https://github.com/ne
 Se você deseja usar uma versão específica do Nextflow, pode definir a variável `NXF_VER` conforme mostrado abaixo:
 
 ```bash
-export NXF_VER=22.04.5
+export NXF_VER=23.04.1
 ```
 
 !!! Note
 
-    Este treinamento requer `NXF_VER=22.04.0`, ou posterior. Esta versão usará a DSL2 como padrão.
+    Este treinamento requer `NXF_VER=23.04.1`, ou posterior. Esta versão usará a DSL2 como padrão.
 
 Execute `nextflow -version` novamente para confirmar que a alteração entrou em vigor.