nextflow-io · vdauwera · Dec 16, 2024 · Dec 16, 2024 · Dec 16, 2024 · Dec 16, 2024
diff --git a/docs/advanced/configuration.md b/docs/advanced/configuration.md
@@ -4,8 +4,8 @@ This is an aspect of Nextflow that can be confusing. There are multiple ways of
 
 This gives us two complications:
 
-- At which location should I be loading a configuration value?
-- Given a particular parameter, how do I know where it was set?
+-   At which location should I be loading a configuration value?
+-   Given a particular parameter, how do I know where it was set?
 
 ## Precedence
 
@@ -152,15 +152,15 @@ The most common use for dynamic process directives is to enable tasks that fail
 
 To enable this, two directives are needed:
 
-- `maxRetries`
-- `errorStrategy`
+-   `maxRetries`
+-   `errorStrategy`
 
 The `errorStrategy` directive determines what action Nextflow should take in the event of a task failure (a non-zero exit code). The available options are:
 
-- `terminate`: Nextflow terminates the execution as soon as an error condition is reported. Pending jobs are killed (default)
-- `finish`: Initiates an orderly pipeline shutdown when an error condition is raised, waiting the completion of any submitted job.
-- `ignore`: Ignores processes execution errors.
-- `retry`: Re-submit for execution a process returning an error condition.
+-   `terminate`: Nextflow terminates the execution as soon as an error condition is reported. Pending jobs are killed (default)
+-   `finish`: Initiates an orderly pipeline shutdown when an error condition is raised, waiting the completion of any submitted job.
+-   `ignore`: Ignores processes execution errors.
+-   `retry`: Re-submit for execution a process returning an error condition.
 
 If the `errorStrategy` is "retry", then it will retry up to the value of `maxRetries` times.
 

diff --git a/docs/advanced/index.md b/docs/advanced/index.md
@@ -16,23 +16,23 @@ Let's get started!
 
 By the end of this course you should:
 
-- Describe commonly used and well understood operators
-- Apply good practices for the propagation of metadata
-- Group and split channels
-- Apply Groovy helper classes to Nextflow scripts
-- Sensibly structure workflows
-- Apply layers of configuration to a workflow
+-   Describe commonly used and well understood operators
+-   Apply good practices for the propagation of metadata
+-   Group and split channels
+-   Apply Groovy helper classes to Nextflow scripts
+-   Sensibly structure workflows
+-   Apply layers of configuration to a workflow
 
 ## Audience & prerequisites
 
 Please note that this is **not** a beginner's workshop and familiarity with Nextflow, the command line, and common file formats is assumed.
 
 **Prerequisites**
 
-- A GitHub account
-- Experience with command line
-- Familiarity with Nextflow and Groovy
-- An understanding of common file formats
+-   A GitHub account
+-   Experience with command line
+-   Familiarity with Nextflow and Groovy
+-   An understanding of common file formats
 
 ## Follow the training video
 

diff --git a/docs/advanced/introduction.md b/docs/advanced/introduction.md
@@ -14,23 +14,23 @@ Let's get started!
 
 By the end of this course you should:
 
-- Describe commonly used and well understood operators
-- Apply good practices for the propagation of metadata
-- Group and split channels
-- Apply Groovy helper classes to Nextflow scripts
-- Sensibly structure workflows
-- Apply layers of configuration to a workflow
+-   Describe commonly used and well understood operators
+-   Apply good practices for the propagation of metadata
+-   Group and split channels
+-   Apply Groovy helper classes to Nextflow scripts
+-   Sensibly structure workflows
+-   Apply layers of configuration to a workflow
 
 ## Audience & prerequisites
 
 Please note that this is **not** a beginner's workshop and familiarity with Nextflow, the command line, and common file formats is assumed.
 
 **Prerequisites**
 
-- A GitHub account
-- Experience with command line
-- Familiarity with Nextflow and Groovy
-- An understanding of common file formats
+-   A GitHub account
+-   Experience with command line
+-   Familiarity with Nextflow and Groovy
+-   An understanding of common file formats
 
 ## Follow the training video
 

diff --git a/docs/advanced/metadata.md b/docs/advanced/metadata.md
@@ -2,8 +2,8 @@
 
 A central challenge in a lot of batch-style computation is how to ensure the metadata describing a file remains with the file. Two good rules for handling metadata in Nextflow are:
 
-- Metadata should be explicit - be extremely wary of metadata encoded in filenames
-- Metadata should travel through channels with the data in a tuple element.
+-   Metadata should be explicit - be extremely wary of metadata encoded in filenames
+-   Metadata should travel through channels with the data in a tuple element.
 
 ## Metadata Import
 

diff --git a/docs/advanced/support.md b/docs/advanced/support.md
@@ -3,6 +3,6 @@ title: Support
 description: Advanced Nextflow Training Workshop
 ---
 
-- Nextflow official documentation is available at [www.nextflow.io/docs/latest](https://www.nextflow.io/docs/latest/)
-- If you have questions, ask on the Seqera Community Forum at [http://community.seqera.io/](http://community.seqera.io/)
-- If you want to chat about Nextflow or plugin development, check the Nextflow Slack at [https://www.nextflow.io/slack-invite.html](https://www.nextflow.io/slack-invite.html)
+-   Nextflow official documentation is available at [www.nextflow.io/docs/latest](https://www.nextflow.io/docs/latest/)
+-   If you have questions, ask on the Seqera Community Forum at [http://community.seqera.io/](http://community.seqera.io/)
+-   If you want to chat about Nextflow or plugin development, check the Nextflow Slack at [https://www.nextflow.io/slack-invite.html](https://www.nextflow.io/slack-invite.html)
diff --git a/docs/basic_training/cache_and_resume.fr.md b/docs/basic_training/cache_and_resume.fr.md
@@ -90,9 +90,9 @@ nextflow run <script> -w /some/scratch/dir
 
 Le code de hachage des fichiers d'entrée est calculé en utilisant :
 
-- le chemin d'accès complet au fichier
-- la taille du fichier
-- l'horodatage de la dernière modification
+-   le chemin d'accès complet au fichier
+-   la taille du fichier
+-   l'horodatage de la dernière modification
 
 Par conséquent, le simple fait de ** toucher** un fichier invalidera l'exécution de la tâche correspondante.
 

diff --git a/docs/basic_training/cache_and_resume.md b/docs/basic_training/cache_and_resume.md
@@ -90,9 +90,9 @@ nextflow run <script> -w /some/scratch/dir
 
 The hash code for input files is computed using:
 
-- The complete file path
-- The file size
-- The last modified timestamp
+-   The complete file path
+-   The file size
+-   The last modified timestamp
 
 Therefore, just **touching** a file will invalidate the related task execution.
 

diff --git a/docs/basic_training/cache_and_resume.pt.md b/docs/basic_training/cache_and_resume.pt.md
@@ -90,9 +90,9 @@ nextflow run <script> -w /algum/diretorio/de/scratch
 
 O código hash para os arquivos de entrada são computados usando:
 
-- O caminho completo do arquivo
-- O tamanho do arquivo
-- A última marcação de tempo de modificação
+-   O caminho completo do arquivo
+-   O tamanho do arquivo
+-   A última marcação de tempo de modificação
 
 Portanto, o simples uso do **touch** em um arquivo irá invalidar a execução da tarefa relacionada.
 

diff --git a/docs/basic_training/channels.md b/docs/basic_training/channels.md
@@ -21,9 +21,9 @@ Nextflow distinguishes two different kinds of channels: **queue** channels and *
 
 A **queue** channel is an _asynchronous_ unidirectional _FIFO_ queue that connects two processes or operators.
 
-- _asynchronous_ means that operations are non-blocking.
-- _unidirectional_ means that data flows from a producer to a consumer.
-- _FIFO_ means that the data is guaranteed to be delivered in the same order as it is produced. First In, First Out.
+-   _asynchronous_ means that operations are non-blocking.
+-   _unidirectional_ means that data flows from a producer to a consumer.
+-   _FIFO_ means that the data is guaranteed to be delivered in the same order as it is produced. First In, First Out.
 
 A queue channel is implicitly created by process output definitions or using channel factories such as [Channel.of](https://www.nextflow.io/docs/latest/channel.html#of) or [Channel.fromPath](https://www.nextflow.io/docs/latest/channel.html#frompath).
 

diff --git a/docs/basic_training/channels.pt.md b/docs/basic_training/channels.pt.md
@@ -20,9 +20,9 @@ O Nextflow distingue dois tipos diferentes de canais: canais de **fila** e canai
 
 Um canal de _fila_ é uma fila assíncrona unidirecional FIFO (First-in-First-out, o primeiro a entrar, é o primeiro a sair) que conecta dois processos ou operadores.
 
-- _assíncrono_ significa que as operações ocorrem sem bloqueio.
-- _unidirecional_ significa que os dados fluem do gerador para o consumidor.
-- _FIFO_ significa que os dados são entregues na mesma ordem em que são produzidos. Primeiro a entrar, primeiro a sair.
+-   _assíncrono_ significa que as operações ocorrem sem bloqueio.
+-   _unidirecional_ significa que os dados fluem do gerador para o consumidor.
+-   _FIFO_ significa que os dados são entregues na mesma ordem em que são produzidos. Primeiro a entrar, primeiro a sair.
 
 Um canal de fila é criado implicitamente por definições de saída de um processo ou usando fábricas de canal, como o [Channel.of](https://www.nextflow.io/docs/latest/channel.html#of) ou [Channel.fromPath](https://www.nextflow.io/docs/latest/channel.html#frompath).
 

diff --git a/docs/basic_training/config.md b/docs/basic_training/config.md
@@ -347,10 +347,10 @@ singularity.enabled = true
 
 The following protocols are supported:
 
-- `library://` download the container image from the [Singularity Library service](https://cloud.sylabs.io/library).
-- `shub://` download the container image from the [Singularity Hub](https://singularity-hub.org/).
-- `docker://` download the container image from the [Docker Hub](https://hub.docker.com/) and convert it to the Singularity format.
-- `docker-daemon://` pull the container image from a local Docker installation and convert it to a Singularity image file.
+-   `library://` download the container image from the [Singularity Library service](https://cloud.sylabs.io/library).
+-   `shub://` download the container image from the [Singularity Hub](https://singularity-hub.org/).
+-   `docker://` download the container image from the [Docker Hub](https://hub.docker.com/) and convert it to the Singularity format.
+-   `docker-daemon://` pull the container image from a local Docker installation and convert it to a Singularity image file.
 
 !!! warning
 

diff --git a/docs/basic_training/config.pt.md b/docs/basic_training/config.pt.md
@@ -273,10 +273,10 @@ singularity.enabled = true
 
 Os seguintes protocolos são suportados:
 
-- `library://` baixe a imagem do contêiner do [Singularity Library service](https://cloud.sylabs.io/library).
-- `shub://` baixe a imagem do contêiner do [Singularity Hub](https://singularity-hub.org/).
-- `docker://` baixe a imagem do contêiner do [Docker Hub](https://hub.docker.com/) e a converta para o formato Singularity.
-- `docker-daemon://` extraia a imagem do contêiner de uma instalação local do Docker e a converta em um arquivo de imagem Singularity.
+-   `library://` baixe a imagem do contêiner do [Singularity Library service](https://cloud.sylabs.io/library).
+-   `shub://` baixe a imagem do contêiner do [Singularity Hub](https://singularity-hub.org/).
+-   `docker://` baixe a imagem do contêiner do [Docker Hub](https://hub.docker.com/) e a converta para o formato Singularity.
+-   `docker-daemon://` extraia a imagem do contêiner de uma instalação local do Docker e a converta em um arquivo de imagem Singularity.
 
 !!! tip
 

diff --git a/docs/basic_training/containers.md b/docs/basic_training/containers.md
@@ -224,8 +224,8 @@ docker run my-image \
 
 To mount a filesystem within a Docker container, you can use the `--volume` command-line option when running the container. Its argument consists of two fields separated by a colon (:):
 
-- Host source directory path
-- Container target directory path
+-   Host source directory path
+-   Container target directory path
 
 For example:
 

diff --git a/docs/basic_training/debugging.fr.md b/docs/basic_training/debugging.fr.md
@@ -49,15 +49,15 @@ Si cela ne suffit pas, `cd` dans le répertoire de travail de la tâche. Il cont
 
 Le répertoire d'exécution de la tâche contient ces fichiers :
 
-- `.command.sh` : Le script de commande.
-- `.command.run` : La commande enveloppée utilisée pour exécuter la tâche.
-- `.command.out` : La sortie standard complète de la tâche.
-- `.command.err` : L'erreur standard de la tâche complète.
-- `.command.log` : La sortie de l'exécution du wrapper.
-- `.command.begin` : Fichier sentinelle créé dès que la tâche est lancée.
-- `.exitcode` : Un fichier contenant le code de sortie de la tâche.
-- Fichiers d'entrée de la tâche (liens symboliques)
-- Fichiers de sortie de la tâche
+-   `.command.sh` : Le script de commande.
+-   `.command.run` : La commande enveloppée utilisée pour exécuter la tâche.
+-   `.command.out` : La sortie standard complète de la tâche.
+-   `.command.err` : L'erreur standard de la tâche complète.
+-   `.command.log` : La sortie de l'exécution du wrapper.
+-   `.command.begin` : Fichier sentinelle créé dès que la tâche est lancée.
+-   `.exitcode` : Un fichier contenant le code de sortie de la tâche.
+-   Fichiers d'entrée de la tâche (liens symboliques)
+-   Fichiers de sortie de la tâche
 
 Vérifiez que le fichier `.command.sh` contient la commande attendue et que toutes les variables sont correctement résolues.
 

diff --git a/docs/basic_training/debugging.md b/docs/basic_training/debugging.md
@@ -49,15 +49,15 @@ If this is not enough, `cd` into the task work directory. It contains all the fi
 
 The task execution directory contains these files:
 
-- `.command.sh`: The command script.
-- `.command.run`: The command wrapped used to run the task.
-- `.command.out`: The complete task standard output.
-- `.command.err`: The complete task standard error.
-- `.command.log`: The wrapper execution output.
-- `.command.begin`: Sentinel file created as soon as the task is launched.
-- `.exitcode`: A file containing the task exit code.
-- Task input files (symlinks)
-- Task output files
+-   `.command.sh`: The command script.
+-   `.command.run`: The command wrapped used to run the task.
+-   `.command.out`: The complete task standard output.
+-   `.command.err`: The complete task standard error.
+-   `.command.log`: The wrapper execution output.
+-   `.command.begin`: Sentinel file created as soon as the task is launched.
+-   `.exitcode`: A file containing the task exit code.
+-   Task input files (symlinks)
+-   Task output files
 
 Verify that the `.command.sh` file contains the expected command and all variables are correctly resolved.
 

diff --git a/docs/basic_training/debugging.pt.md b/docs/basic_training/debugging.pt.md
@@ -50,15 +50,15 @@ Se isso não for o suficiente, use `cd` para entrar no diretório de trabalho da
 
 O diretório de execução da tarefa possui os seguintes arquivos:
 
-- `.command.sh`: O script do comando.
-- `.command.run`: Um wrapper do comando usado para executar a tarefa.
-- `.command.out`: A saída padrão completa da tarefa.
-- `.command.err`: O erro padrão completo da tarefa.
-- `.command.log`: A saída do wrapper de execução.
-- `.command.begin`: Um arquivo sentinela criado no momento que a tarefa é iniciada.
-- `.exitcode`: Um arquivo contendo o código de saída da tarefa.
-- Os arquivos de entrada da tarefa (links simbólicas)
-- Os arquivos de saída da tarefa
+-   `.command.sh`: O script do comando.
+-   `.command.run`: Um wrapper do comando usado para executar a tarefa.
+-   `.command.out`: A saída padrão completa da tarefa.
+-   `.command.err`: O erro padrão completo da tarefa.
+-   `.command.log`: A saída do wrapper de execução.
+-   `.command.begin`: Um arquivo sentinela criado no momento que a tarefa é iniciada.
+-   `.exitcode`: Um arquivo contendo o código de saída da tarefa.
+-   Os arquivos de entrada da tarefa (links simbólicas)
+-   Os arquivos de saída da tarefa
 
 Certifique-se que o arquivo `.command.sh` contém o comando esperado e que todas as variáveis
 foram substituídas pelos valores desejados.

diff --git a/docs/basic_training/executors.fr.md b/docs/basic_training/executors.fr.md
@@ -84,8 +84,8 @@ sbatch launch_nf.sh /home/my_user/path/my_workflow.nf /home/my_user/path/my_conf
 Vous trouverez plus de détails sur l'exemple ci-dessus [ici](https://lescailab.unipv.it/guides/eos_guide/use_nextflow.html#large-testing-or-production).
 Vous trouverez d'autres conseils pour l'exécution de Nextflow sur HPC dans les articles de blog suivants :
 
-- [5 astuces Nextflow pour les utilisateurs HPC](https://www.nextflow.io/blog/2021/5_tips_for_hpc_users.html)
-- [Cinq astuces supplémentaires pour les utilisateurs de Nextflow sur le HPC](https://www.nextflow.io/blog/2021/5-more-tips-for-nextflow-user-on-hpc.html)
+-   [5 astuces Nextflow pour les utilisateurs HPC](https://www.nextflow.io/blog/2021/5_tips_for_hpc_users.html)
+-   [Cinq astuces supplémentaires pour les utilisateurs de Nextflow sur le HPC](https://www.nextflow.io/blog/2021/5-more-tips-for-nextflow-user-on-hpc.html)
 
 ### Configurer le processus par nom
 

diff --git a/docs/basic_training/executors.md b/docs/basic_training/executors.md
@@ -87,8 +87,8 @@ sbatch launch_nf.sh /home/my_user/path/my_workflow.nf /home/my_user/path/my_conf
 You can find more details about the example above [here](https://lescailab.unipv.it/guides/eos_guide/use_nextflow.html#large-testing-or-production).
 You can find more tips for running Nextflow on HPC in the following blog posts:
 
-- [5 Nextflow Tips for HPC Users](https://www.nextflow.io/blog/2021/5_tips_for_hpc_users.html)
-- [Five more tips for Nextflow user on HPC](https://www.nextflow.io/blog/2021/5-more-tips-for-nextflow-user-on-hpc.html)
+-   [5 Nextflow Tips for HPC Users](https://www.nextflow.io/blog/2021/5_tips_for_hpc_users.html)
+-   [Five more tips for Nextflow user on HPC](https://www.nextflow.io/blog/2021/5-more-tips-for-nextflow-user-on-hpc.html)
 
 ### Configure process by name
 

diff --git a/docs/basic_training/executors.pt.md b/docs/basic_training/executors.pt.md
@@ -83,8 +83,8 @@ sbatch launch_nf.sh /home/meu_usuario/caminho/meu_fluxo_de_trabalho.nf /home/meu
 
 Você pode encontrar mais detalhes sobre o exemplo acima [aqui](https://lescailab.unipv.it/guides/eos_guide/use_nextflow.html#large-testing-or-production). Você também poderá encontrar mais dicas de como executar o Nextflow em HPC nos seguintes posts de blog:
 
-- [5 Nextflow Tips for HPC Users](https://www.nextflow.io/blog/2021/5_tips_for_hpc_users.html)
-- [Five more tips for Nextflow user on HPC](https://www.nextflow.io/blog/2021/5-more-tips-for-nextflow-user-on-hpc.html)
+-   [5 Nextflow Tips for HPC Users](https://www.nextflow.io/blog/2021/5_tips_for_hpc_users.html)
+-   [Five more tips for Nextflow user on HPC](https://www.nextflow.io/blog/2021/5-more-tips-for-nextflow-user-on-hpc.html)
 
 ### Configure processos por nome
 

diff --git a/docs/basic_training/index.es.md b/docs/basic_training/index.es.md
@@ -29,11 +29,11 @@ Realizamos un evento de capacitación en línea gratuito para este curso aproxim
 Si el inglés no es su idioma preferido, puede resultarle útil seguir la capacitación del [evento de marzo de 2023](https://nf-co.re/events/2023/training-march-2023), que realizamos en múltiples idiomas.
 Tenga en cuenta que algunas partes del material de capacitación pueden haberse actualizado desde que se registró.
 
-- :flag_gb: [En Inglés](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
-- :flag_in: [En Hindú](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
-- :flag_es: [En Español](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
-- :flag_pt: [En Portugues](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
-- :flag_fr: [En Francés](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
+-   :flag_gb: [En Inglés](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
+-   :flag_in: [En Hindú](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
+-   :flag_es: [En Español](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
+-   :flag_pt: [En Portugues](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
+-   :flag_fr: [En Francés](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
 
 ## Descripción general