Fix linting issues

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.
 

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
 

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
 

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
 

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)

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.
 

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.
 

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.
 

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).
 

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).
 

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
 

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
 

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:
 

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.
 

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.
 

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.

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
 

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
 

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
 

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