diff --git a/docs/advanced/configuration.md b/docs/advanced/configuration.md
index 47306e75..dd1b30c7 100644
--- 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
index 1de33996..89e363df 100644
--- a/docs/advanced/index.md
+++ b/docs/advanced/index.md
@@ -16,12 +16,12 @@ 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
 
@@ -29,10 +29,10 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 
 **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
index f523e312..a5967227 100644
--- a/docs/advanced/introduction.md
+++ b/docs/advanced/introduction.md
@@ -14,12 +14,12 @@ 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
 
@@ -27,10 +27,10 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 
 **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
index b0f02767..294ac86c 100644
--- 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
index c4353e34..6cf585fd 100644
--- 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
index 424c9e9d..ea993951 100644
--- 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
index 48466094..264f829f 100644
--- 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
index db91f461..274dd22e 100644
--- 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
index fdfd7777..50ff896f 100644
--- 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
index f3cd2d92..c5e5c3af 100644
--- 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
index dcd1776b..7b2aab99 100644
--- 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
index fa0f3994..ef638975 100644
--- 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
index 46942c68..05c544f2 100644
--- 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
index a1674de7..e5fc3100 100644
--- 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
index 25281094..9507684a 100644
--- 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
index 13946890..e528ae1a 100644
--- 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
index 0002e4a4..ad27e2d2 100644
--- 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
index 7f30159e..dba78018 100644
--- 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
index 79b8a752..f82d0d39 100644
--- 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
index 2502d1ac..caa9cb4a 100644
--- 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
 
diff --git a/docs/basic_training/index.fr.md b/docs/basic_training/index.fr.md
index b94a16a9..2202ffe5 100644
--- a/docs/basic_training/index.fr.md
+++ b/docs/basic_training/index.fr.md
@@ -29,11 +29,11 @@ Nous organisons un événement de formation en ligne gratuit pour ce cours envir
 Si l'anglais n'est pas votre langue préférée, vous trouverez peut-être utile de suivre la formation de [l'événement de mars 2023](https://nf-co.re/events/2023/training-march-2023), que nous avons organisé plusieurs langues.
 Veuillez noter que certaines parties du matériel de formation peuvent avoir été mises à jour depuis leur enregistrement.
 
--   :flag_gb: [En Anglais](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
--   :flag_in: [En Hindi](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
--   :flag_es: [En Espagnol](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
--   :flag_pt: [En Portugais](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
--   :flag_fr: [En Français](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
+- :flag_gb: [En Anglais](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
+- :flag_in: [En Hindi](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
+- :flag_es: [En Espagnol](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
+- :flag_pt: [En Portugais](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
+- :flag_fr: [En Français](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
 
 ## Aperçu
 
diff --git a/docs/basic_training/index.md b/docs/basic_training/index.md
index ca1d0ec9..bf224d32 100644
--- a/docs/basic_training/index.md
+++ b/docs/basic_training/index.md
@@ -10,11 +10,11 @@ Let's get started!
 
 By the end of this course you should:
 
--   Write simple Nextflow workflows
--   Describe the Nextflow concepts of Channels, Processes and Operators
--   Have an understanding of containerized workflows
--   Understand the different execution platforms supported by Nextflow
--   Describe the Nextflow community and ecosystem
+- Write simple Nextflow workflows
+- Describe the Nextflow concepts of Channels, Processes and Operators
+- Have an understanding of containerized workflows
+- Understand the different execution platforms supported by Nextflow
+- Describe the Nextflow community and ecosystem
 
 ## Audience & prerequisites
 
@@ -22,9 +22,9 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 
 **Prerequisites**
 
--   A GitHub account
--   Experience with command line
--   An understanding of common file formats
+- A GitHub account
+- Experience with command line
+- An understanding of common file formats
 
 ## Follow the training videos
 
@@ -42,8 +42,8 @@ You can watch the recording of the most recent training ([March, 2024](https://n
 
 If English is not your preferred language, you may find it useful to follow the training from the [March 2023 event](https://nf-co.re/events/2023/training-march-2023), which is available in multiple languages.
 
--   :flag_gb: [English recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
--   :flag_in: [Hindi recording](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
--   :flag_es: [Spanish recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
--   :flag_pt: [Portuguese recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
--   :flag_fr: [French recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
+- :flag_gb: [English recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
+- :flag_in: [Hindi recording](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
+- :flag_es: [Spanish recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
+- :flag_pt: [Portuguese recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
+- :flag_fr: [French recording](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
diff --git a/docs/basic_training/index.pt.md b/docs/basic_training/index.pt.md
index 60e90840..10016e6f 100644
--- a/docs/basic_training/index.pt.md
+++ b/docs/basic_training/index.pt.md
@@ -29,11 +29,11 @@ Realizamos um evento de treinamento online gratuito para este curso aproximadame
 Se o inglês não for seu idioma preferido, pode ser útil seguir o treinamento do [evento de março de 2023](https://nf-co.re/events/2023/training-march-2023), que realizamos em múltiplos idiomas.
 Observe que algumas partes do material de treinamento podem ter sido atualizadas desde que foi gravado.
 
--   :flag_gb: [Em Inglês](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
--   :flag_in: [Em Hindu](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
--   :flag_es: [Em Espanhol](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
--   :flag_pt: [Em Português](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
--   :flag_fr: [Em Francês](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
+- :flag_gb: [Em Inglês](https://youtube.com/playlist?list=PL3xpfTVZLcNhoWxHR0CS-7xzu5eRT8uHo)
+- :flag_in: [Em Hindu](https://youtube.com/playlist?list=PL3xpfTVZLcNikun1FrSvtXW8ic32TciTJ)
+- :flag_es: [Em Espanhol](https://youtube.com/playlist?list=PL3xpfTVZLcNhSlCWVoa3GURacuLWeFc8O)
+- :flag_pt: [Em Português](https://youtube.com/playlist?list=PL3xpfTVZLcNhi41yDYhyHitUhIcUHIbJg)
+- :flag_fr: [Em Francês](https://youtube.com/playlist?list=PL3xpfTVZLcNhiv9SjhoA1EDOXj9nzIqdS)
 
 ## Visão geral
 
diff --git a/docs/basic_training/intro.fr.md b/docs/basic_training/intro.fr.md
index 776435ec..bd41c8d5 100644
--- a/docs/basic_training/intro.fr.md
+++ b/docs/basic_training/intro.fr.md
@@ -12,9 +12,9 @@ Il est conçu autour de l'idée que la plateforme Linux est la _lingua franca_ d
 
 Nextflow étend cette approche en ajoutant la possibilité de définir des interactions complexes entre les programmes et un environnement de calcul parallèle de haut niveau, basé sur le modèle de programmation par flux de données. Les principales caractéristiques de Nextflow sont les suivantes:
 
--   Portabilité et reproductibilité du workflow
--   la scalabilité de la parallélisation et du déploiement
--   Intégration des outils, systèmes et normes industrielles existants
+- Portabilité et reproductibilité du workflow
+- la scalabilité de la parallélisation et du déploiement
+- Intégration des outils, systèmes et normes industrielles existants
 
 ### Processus et canaux
 
diff --git a/docs/basic_training/intro.md b/docs/basic_training/intro.md
index 1fdf234c..9da123ab 100644
--- a/docs/basic_training/intro.md
+++ b/docs/basic_training/intro.md
@@ -11,9 +11,9 @@ It is designed around the idea that the Linux platform is the _lingua franca_ of
 
 Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment, based on the dataflow programming model. Nextflow’s core features are:
 
--   Workflow portability and reproducibility
--   Scalability of parallelization and deployment
--   Integration of existing tools, systems, and industry standards
+- Workflow portability and reproducibility
+- Scalability of parallelization and deployment
+- Integration of existing tools, systems, and industry standards
 
 ## Processes and Channels
 
diff --git a/docs/basic_training/intro.pt.md b/docs/basic_training/intro.pt.md
index bd0253cc..dca30b2e 100644
--- a/docs/basic_training/intro.pt.md
+++ b/docs/basic_training/intro.pt.md
@@ -12,9 +12,9 @@ Ele foi projetado com base na ideia de que a plataforma Linux é a _língua fran
 
 O Nextflow estende essa abordagem, adicionando a capacidade de definir interações complexas entre programas e um ambiente de computação paralela de alto nível, baseado no modelo de programação Dataflow. Os principais recursos do Nextflow são:
 
--   Portabilidade e reprodutibilidade de fluxos de trabalho
--   Escalabilidade na paralelização e na implantação
--   Integração de ferramentas já existentes, sistemas e padrões da indústria
+- Portabilidade e reprodutibilidade de fluxos de trabalho
+- Escalabilidade na paralelização e na implantação
+- Integração de ferramentas já existentes, sistemas e padrões da indústria
 
 ### Processos e Canais
 
diff --git a/docs/basic_training/modules.md b/docs/basic_training/modules.md
index 641a01bb..46b13c40 100644
--- a/docs/basic_training/modules.md
+++ b/docs/basic_training/modules.md
@@ -19,10 +19,10 @@ Components defined in the module script can be imported into other Nextflow scri
 
 Using the `hello.nf` example, you can achieve this by:
 
--   Creating a file called `modules.nf` in the top-level directory.
--   Copying and pasting the two process definitions for `SPLITLETTERS` and `CONVERTTOUPPER` into `modules.nf`.
--   Removing the `process` definitions in the `hello.nf` script.
--   Importing the processes from `modules.nf` within the `hello.nf` script anywhere above the `workflow` definition:
+- Creating a file called `modules.nf` in the top-level directory.
+- Copying and pasting the two process definitions for `SPLITLETTERS` and `CONVERTTOUPPER` into `modules.nf`.
+- Removing the `process` definitions in the `hello.nf` script.
+- Importing the processes from `modules.nf` within the `hello.nf` script anywhere above the `workflow` definition:
 
 ```groovy linenums="1" title="hello.nf"
 include { SPLITLETTERS   } from './modules.nf'
diff --git a/docs/basic_training/modules.pt.md b/docs/basic_training/modules.pt.md
index 815c4896..8cd3aa07 100644
--- a/docs/basic_training/modules.pt.md
+++ b/docs/basic_training/modules.pt.md
@@ -18,10 +18,10 @@ Os componentes definidos no script do módulo podem ser importados para outros s
 
 Usando o exemplo `hello.nf`, podemos fazer isso:
 
--   Criando um arquivo chamado `modules.nf` no mesmo diretório do `hello.nf`.
--   Copiando e colando as duas definições de processo para `SPLITLETTERS` e `CONVERTTOUPPER` em `modules.nf`.
--   Removendo as definições `process` no script `hello.nf`.
--   Importando os processos de `modules.nf` dentro do script `hello.nf` em qualquer lugar acima da definição de `workflow`:
+- Criando um arquivo chamado `modules.nf` no mesmo diretório do `hello.nf`.
+- Copiando e colando as duas definições de processo para `SPLITLETTERS` e `CONVERTTOUPPER` em `modules.nf`.
+- Removendo as definições `process` no script `hello.nf`.
+- Importando os processos de `modules.nf` dentro do script `hello.nf` em qualquer lugar acima da definição de `workflow`:
 
 ```groovy linenums="1"
 include { SPLITLETTERS } from './modules.nf'
diff --git a/docs/basic_training/processes.md b/docs/basic_training/processes.md
index 59c5c9cf..8dd395c6 100644
--- a/docs/basic_training/processes.md
+++ b/docs/basic_training/processes.md
@@ -758,9 +758,9 @@ Prints the following:
 
 Some caveats on glob pattern behavior:
 
--   Input files are not included in the list of possible matches
--   Glob pattern matches both files and directory paths
--   When a two stars pattern `**` is used to recourse across directories, only file paths are matched i.e., directories are not included in the result list.
+- Input files are not included in the list of possible matches
+- Glob pattern matches both files and directory paths
+- When a two stars pattern `**` is used to recourse across directories, only file paths are matched i.e., directories are not included in the result list.
 
 !!! question "Exercise"
 
diff --git a/docs/basic_training/processes.pt.md b/docs/basic_training/processes.pt.md
index 304257bc..971e0b99 100644
--- a/docs/basic_training/processes.pt.md
+++ b/docs/basic_training/processes.pt.md
@@ -405,9 +405,9 @@ workflow {
 
 Ambos os canais emitem três valores, portanto o processo é executado três vezes, cada vez com um par diferente:
 
--   `(1, a)`
--   `(2, b)`
--   `(3, c)`
+- `(1, a)`
+- `(2, b)`
+- `(3, c)`
 
 O que está acontecendo é que o processo espera até que haja uma configuração de entrada completa, ou seja, recebe um valor de entrada de todos os canais declarados como entrada.
 
@@ -675,9 +675,9 @@ Arquivo: pedaco_ad => a
 
 Algumas advertências sobre o comportamento de padrões de glob:
 
--   Os arquivos de entrada não estão incluídos na lista de possíveis correspondências
--   O padrão glob corresponde tanto a arquivos quanto caminhos de diretório
--   Quando um padrão de duas estrelas `**` é usado para acessar os diretórios, apenas os caminhos de arquivo são correspondidos, ou seja, os diretórios não são incluídos na lista de resultados.
+- Os arquivos de entrada não estão incluídos na lista de possíveis correspondências
+- O padrão glob corresponde tanto a arquivos quanto caminhos de diretório
+- Quando um padrão de duas estrelas `**` é usado para acessar os diretórios, apenas os caminhos de arquivo são correspondidos, ou seja, os diretórios não são incluídos na lista de resultados.
 
 !!! exercise
 
diff --git a/docs/basic_training/rnaseq_pipeline.fr.md b/docs/basic_training/rnaseq_pipeline.fr.md
index f86c4bc1..1d994994 100644
--- a/docs/basic_training/rnaseq_pipeline.fr.md
+++ b/docs/basic_training/rnaseq_pipeline.fr.md
@@ -570,7 +570,7 @@ Les tags permettent un contrôle précis des modifications apportées à vos fic
 
 ## Plus de ressources
 
--   [Documentation Nextflow](http://docs.nextflow.io) - L'accueil de la documentation Nextflow.
--   [Modèles Nextflow](https://github.com/nextflow-io/patterns) - Une collection de modèles de mise en œuvre de Nextflow.
--   [CalliNGS-NF](https://github.com/CRG-CNAG/CalliNGS-NF) - Un workflow d'appel de variants mettant en œuvre les meilleures pratiques de GATK.
--   [nf-core](http://nf-co.re/) - Une collection communautaire de workflows génomiques prêts à la production.
+- [Documentation Nextflow](http://docs.nextflow.io) - L'accueil de la documentation Nextflow.
+- [Modèles Nextflow](https://github.com/nextflow-io/patterns) - Une collection de modèles de mise en œuvre de Nextflow.
+- [CalliNGS-NF](https://github.com/CRG-CNAG/CalliNGS-NF) - Un workflow d'appel de variants mettant en œuvre les meilleures pratiques de GATK.
+- [nf-core](http://nf-co.re/) - Une collection communautaire de workflows génomiques prêts à la production.
diff --git a/docs/basic_training/rnaseq_pipeline.md b/docs/basic_training/rnaseq_pipeline.md
index e3172455..80afbf87 100644
--- a/docs/basic_training/rnaseq_pipeline.md
+++ b/docs/basic_training/rnaseq_pipeline.md
@@ -115,9 +115,9 @@ Nextflow allows the execution of any command or script by using a `process` defi
 
 A `process` is defined by providing three main declarations:
 
--   [`input`](https://www.nextflow.io/docs/latest/process.html#inputs)
--   [`output`](https://www.nextflow.io/docs/latest/process.html#outputs)
--   [`script`](https://www.nextflow.io/docs/latest/process.html#script)
+- [`input`](https://www.nextflow.io/docs/latest/process.html#inputs)
+- [`output`](https://www.nextflow.io/docs/latest/process.html#outputs)
+- [`script`](https://www.nextflow.io/docs/latest/process.html#script)
 
 To add a transcriptome `INDEX` processing step to your pipeline, you will need to add the following code block to your `script1.nf`. Alternatively, this code block has already been added to `script2.nf`.
 
diff --git a/docs/basic_training/rnaseq_pipeline.pt.md b/docs/basic_training/rnaseq_pipeline.pt.md
index f901556e..3182da1f 100644
--- a/docs/basic_training/rnaseq_pipeline.pt.md
+++ b/docs/basic_training/rnaseq_pipeline.pt.md
@@ -570,7 +570,7 @@ As etiquetas permitem o controle preciso das alterações nos arquivos e depend
 
 ## Mais recursos
 
--   [Documentação do Nextflow](http://docs.nextflow.io) - A página inicial dos documentos do Nextflow.
--   [Nextflow patterns](https://github.com/nextflow-io/patterns) - Uma coleção de padrões de implementação do Nextflow.
--   [CalliNGS-NF](https://github.com/CRG-CNAG/CalliNGS-NF) - Um fluxo de trabalho de chamada de variante implementando as melhores práticas recomendadas do GATK.
--   [nf-core](http://nf-co.re/) - Uma coleção comunitária de fluxos de trabalho genômicos prontos para produção.
+- [Documentação do Nextflow](http://docs.nextflow.io) - A página inicial dos documentos do Nextflow.
+- [Nextflow patterns](https://github.com/nextflow-io/patterns) - Uma coleção de padrões de implementação do Nextflow.
+- [CalliNGS-NF](https://github.com/CRG-CNAG/CalliNGS-NF) - Um fluxo de trabalho de chamada de variante implementando as melhores práticas recomendadas do GATK.
+- [nf-core](http://nf-co.re/) - Uma coleção comunitária de fluxos de trabalho genômicos prontos para produção.
diff --git a/docs/basic_training/seqera_platform.fr.md b/docs/basic_training/seqera_platform.fr.md
index 1f746e63..22b32c7d 100644
--- a/docs/basic_training/seqera_platform.fr.md
+++ b/docs/basic_training/seqera_platform.fr.md
@@ -11,10 +11,10 @@ Seqera Platform, anciennement connu sous le nom Nextflow Tower, est le poste de
 
 Les principales caractéristiques de Seqera Platform sont les suivantes
 
--   Le lancement de pipelines préconfigurés en toute simplicité.
--   L'intégration programmatique pour répondre aux besoins d'une organisation.
--   La publication de pipelines dans des espaces de travail partagés.
--   La gestion de l'infrastructure nécessaire à l'exécution d'analyses de données à grande échelle.
+- Le lancement de pipelines préconfigurés en toute simplicité.
+- L'intégration programmatique pour répondre aux besoins d'une organisation.
+- La publication de pipelines dans des espaces de travail partagés.
+- La gestion de l'infrastructure nécessaire à l'exécution d'analyses de données à grande échelle.
 
 !!! conseil
 
diff --git a/docs/basic_training/seqera_platform.md b/docs/basic_training/seqera_platform.md
index 070e2025..e85f413a 100644
--- a/docs/basic_training/seqera_platform.md
+++ b/docs/basic_training/seqera_platform.md
@@ -9,10 +9,10 @@ Seqera Platform, previously known as Nextflow Tower, is the centralized command
 
 Seqera core features include:
 
--   The launching of pre-configured pipelines with ease.
--   Programmatic integration to meet the needs of an organization.
--   Publishing pipelines to shared workspaces.
--   Management of the infrastructure required to run data analysis at scale.
+- The launching of pre-configured pipelines with ease.
+- Programmatic integration to meet the needs of an organization.
+- Publishing pipelines to shared workspaces.
+- Management of the infrastructure required to run data analysis at scale.
 
 !!! tip
 
diff --git a/docs/basic_training/seqera_platform.pt.md b/docs/basic_training/seqera_platform.pt.md
index 77661519..83637228 100644
--- a/docs/basic_training/seqera_platform.pt.md
+++ b/docs/basic_training/seqera_platform.pt.md
@@ -11,10 +11,10 @@ A Seqera Platform, conhecida anteriormente como Nextflow Tower, é o posto de co
 
 Os principais recursos da Seqera Platform incluem:
 
--   O lançamento de pipelines pré-configurados com facilidade.
--   Integração programática para atender às necessidades de uma organização.
--   Disponibilização pipelines em áreas de trabalho compartilhadas.
--   Gerenciamento da infraestrutura necessária para executar análise de dados em escala.
+- O lançamento de pipelines pré-configurados com facilidade.
+- Integração programática para atender às necessidades de uma organização.
+- Disponibilização pipelines em áreas de trabalho compartilhadas.
+- Gerenciamento da infraestrutura necessária para executar análise de dados em escala.
 
 !!! tip
 
diff --git a/docs/basic_training/setup.fr.md b/docs/basic_training/setup.fr.md
index c0034c82..83b43c5f 100644
--- a/docs/basic_training/setup.fr.md
+++ b/docs/basic_training/setup.fr.md
@@ -18,18 +18,18 @@ Nextflow peut être utilisé sur n'importe quel système compatible POSIX (Linux
 
 #### Exigences
 
--   Bash
--   [Java 11 (or later, up to 18)](https://www.oracle.com/technetwork/java/javase/downloads/index.html)
--   Git
--   [Docker](https://docs.docker.com/get-docker/)
+- Bash
+- [Java 11 (or later, up to 18)](https://www.oracle.com/technetwork/java/javase/downloads/index.html)
+- Git
+- [Docker](https://docs.docker.com/get-docker/)
 
 #### Exigences optionnelles pour ce tutoriel
 
--   [Singularity](https://github.com/sylabs/singularity) 2.5.x (ou plus)
--   [Conda](https://conda.io/) 4.5 (ou plus)
--   [Graphviz](http://www.graphviz.org/)
--   [AWS CLI](https://aws.amazon.com/cli/)
--   Un environnement AWS Batch configuré
+- [Singularity](https://github.com/sylabs/singularity) 2.5.x (ou plus)
+- [Conda](https://conda.io/) 4.5 (ou plus)
+- [Graphviz](http://www.graphviz.org/)
+- [AWS CLI](https://aws.amazon.com/cli/)
+- Un environnement AWS Batch configuré
 
 ### Télécharger Nextflow
 
@@ -85,17 +85,17 @@ Un environnement de développement Nextflow préconfiguré est disponible via Gi
 
 #### Exigences
 
--   Un compte GitHub
--   Navigateur web (Google Chrome, Firefox)
--   Une connexion internet
+- Un compte GitHub
+- Navigateur web (Google Chrome, Firefox)
+- Une connexion internet
 
 ### Démarrage rapide de Gitpod
 
 Pour exécuter Gitpod :
 
--   Cliquez sur l'URL suivante : <https://gitpod.io/#https://github.com/nextflow-io/training>
-    -   Il s'agit de l'URL de notre repositoire GitHub, préfixée par `https://gitpod.io/#`.
--   Connectez-vous à votre compte GitHub (et autorisez l'accès).
+- Cliquez sur l'URL suivante : <https://gitpod.io/#https://github.com/nextflow-io/training>
+    - Il s'agit de l'URL de notre repositoire GitHub, préfixée par `https://gitpod.io/#`.
+- Connectez-vous à votre compte GitHub (et autorisez l'accès).
 
 Une fois que vous vous êtes connecté, Gitpod devrait se charger (sautez le prebuild si on vous le demande).
 
@@ -105,9 +105,9 @@ Vous devriez maintenant voir quelque chose de similaire à ce qui suit :
 
 ![Gitpod welcome](img/gitpod.welcome.png)
 
--   **La barre latérale** vous permet de personnaliser votre environnement Gitpod et d'effectuer des tâches de base (copier, coller, ouvrir des fichiers, rechercher, git, etc.) Cliquez sur le bouton Explorer pour voir quels fichiers se trouvent dans ce dépôt.
--   **Le terminal** vous permet d'exécuter tous les programmes du repositoire. Par exemple, `nextflow` et `docker` sont installés et peuvent être exécutés
--   **La fenêtre principale** vous permet de visualiser et d'éditer des fichiers. En cliquant sur un fichier dans l'explorateur, vous l'ouvrez dans la fenêtre principale. Vous devriez également voir le materiel du navigateur de formation nf-training (<https://training.nextflow.io
+- **La barre latérale** vous permet de personnaliser votre environnement Gitpod et d'effectuer des tâches de base (copier, coller, ouvrir des fichiers, rechercher, git, etc.) Cliquez sur le bouton Explorer pour voir quels fichiers se trouvent dans ce dépôt.
+- **Le terminal** vous permet d'exécuter tous les programmes du repositoire. Par exemple, `nextflow` et `docker` sont installés et peuvent être exécutés
+- **La fenêtre principale** vous permet de visualiser et d'éditer des fichiers. En cliquant sur un fichier dans l'explorateur, vous l'ouvrez dans la fenêtre principale. Vous devriez également voir le materiel du navigateur de formation nf-training (<https://training.nextflow.io
 
 Pour vérifier que l'environnement fonctionne correctement, tapez ce qui suit dans le terminal :
 
@@ -127,9 +127,9 @@ Encoding: UTF-8 (UTF-8)
 
 ### Resources de Gitpod
 
--   Gitpod vous offre 500 crédits gratuits par mois, ce qui équivaut à 50 heures d'utilisation gratuite de l'environnement en utilisant l'espace de travail standard (jusqu'à 4 cœurs, 8 Go de RAM et 30 Go d'espace de stockage).
--   Il existe également une option de grand espace de travail qui vous permet d'utiliser jusqu'à 8 cœurs, 16 Go de RAM et 50 Go d'espace de stockage. Cependant, le grand espace de travail utilisera vos crédits gratuits plus rapidement et vous aurez moins d'heures d'accès à cet espace.
--   Gitpod s'arrête au bout de 30 minutes d'inactivité et conserve les modifications jusqu'à deux semaines (voir la section suivante pour réouvrir une session interrompue).
+- Gitpod vous offre 500 crédits gratuits par mois, ce qui équivaut à 50 heures d'utilisation gratuite de l'environnement en utilisant l'espace de travail standard (jusqu'à 4 cœurs, 8 Go de RAM et 30 Go d'espace de stockage).
+- Il existe également une option de grand espace de travail qui vous permet d'utiliser jusqu'à 8 cœurs, 16 Go de RAM et 50 Go d'espace de stockage. Cependant, le grand espace de travail utilisera vos crédits gratuits plus rapidement et vous aurez moins d'heures d'accès à cet espace.
+- Gitpod s'arrête au bout de 30 minutes d'inactivité et conserve les modifications jusqu'à deux semaines (voir la section suivante pour réouvrir une session interrompue).
 
 Voir [gitpod.io](https://www.gitpod.io) pour plus de details.
 
diff --git a/docs/basic_training/setup.pt.md b/docs/basic_training/setup.pt.md
index 965e0d3e..cd38a600 100644
--- a/docs/basic_training/setup.pt.md
+++ b/docs/basic_training/setup.pt.md
@@ -18,18 +18,18 @@ O Nextflow pode ser usado em qualquer sistema compatível com POSIX (Linux, macO
 
 #### Requisitos
 
--   Bash
--   [Java 11 (ou uma versão posterior, até a 18)](https://www.oracle.com/technetwork/java/javase/downloads/index.html)
--   Git
--   [Docker](https://docs.docker.com/get-docker/)
+- Bash
+- [Java 11 (ou uma versão posterior, até a 18)](https://www.oracle.com/technetwork/java/javase/downloads/index.html)
+- Git
+- [Docker](https://docs.docker.com/get-docker/)
 
 #### Requisitos opcionais para este tutorial
 
--   [Singularity](https://github.com/sylabs/singularity) 2.5.x (ou uma versão posterior)
--   [Conda](https://conda.io/) 4.5 (ou uma versão posterior)
--   [Graphviz](http://www.graphviz.org/)
--   [AWS CLI](https://aws.amazon.com/cli/)
--   Um ambiente de computação do AWS Batch configurado
+- [Singularity](https://github.com/sylabs/singularity) 2.5.x (ou uma versão posterior)
+- [Conda](https://conda.io/) 4.5 (ou uma versão posterior)
+- [Graphviz](http://www.graphviz.org/)
+- [AWS CLI](https://aws.amazon.com/cli/)
+- Um ambiente de computação do AWS Batch configurado
 
 ### Baixe o Nextflow
 
@@ -85,17 +85,17 @@ Um ambiente de desenvolvimento Nextflow pré-configurado está disponível no Gi
 
 #### Requisitos
 
--   Uma conta no GitHub
--   Navegador Web (Google Chrome, Firefox)
--   Conexão com a Internet
+- Uma conta no GitHub
+- Navegador Web (Google Chrome, Firefox)
+- Conexão com a Internet
 
 ### Gitpod quick start
 
 Para executar o Gitpod:
 
--   Clique na URL a seguir: <https://gitpod.io/#https://github.com/nextflow-io/training>
-    -   Essa URL é o link do repositório do treinamento no GitHub, prefixado com `https://gitpod.io/#`
--   Faça login na sua conta do GitHub (e permita a autorização).
+- Clique na URL a seguir: <https://gitpod.io/#https://github.com/nextflow-io/training>
+    - Essa URL é o link do repositório do treinamento no GitHub, prefixado com `https://gitpod.io/#`
+- Faça login na sua conta do GitHub (e permita a autorização).
 
 Depois de fazer login, o Gitpod deve carregar (pule a pré-compilação, se solicitado).
 
@@ -105,9 +105,9 @@ Agora você deve ver algo semelhante a imagem a seguir:
 
 ![Gitpod welcome](img/gitpod.welcome.png)
 
--   **A barra lateral** permite que você personalize seu ambiente Gitpod e execute tarefas básicas (copiar, colar, abrir arquivos, pesquisar, git, etc.). Clique no botão Explorer para ver quais arquivos estão neste repositório.
--   **O terminal** permite que você execute todos os programas mencionados no repositório. Por exemplo, tanto `nextflow` quanto `docker` estão instalados e podem ser executados.
--   **A janela principal** permite visualizar e editar arquivos. Clique em um arquivo no explorer para abri-lo na janela principal. Você também deve ver o material de treinamento em uma das janelas (<https://training.nextflow.io/>).
+- **A barra lateral** permite que você personalize seu ambiente Gitpod e execute tarefas básicas (copiar, colar, abrir arquivos, pesquisar, git, etc.). Clique no botão Explorer para ver quais arquivos estão neste repositório.
+- **O terminal** permite que você execute todos os programas mencionados no repositório. Por exemplo, tanto `nextflow` quanto `docker` estão instalados e podem ser executados.
+- **A janela principal** permite visualizar e editar arquivos. Clique em um arquivo no explorer para abri-lo na janela principal. Você também deve ver o material de treinamento em uma das janelas (<https://training.nextflow.io/>).
 
 Para testar se o ambiente está funcionando corretamente, digite o seguinte comando no terminal:
 
@@ -127,9 +127,9 @@ Encoding: UTF-8 (UTF-8)
 
 ### Recursos do Gitpod
 
--   O Gitpod oferece 500 créditos gratuitos por mês, o que equivale a 50 horas de tempo de execução no ambiente de trabalho padrão (até 4 núcleos, 8 GB de RAM e 30 GB de armazenamento).
--   Há também uma opção de ambiente de trabalho que oferece até 8 núcleos, 16 GB de RAM e 50 GB de armazenamento. No entanto, o ambiente de trabalho grande usará seus créditos gratuitos mais rapidamente e você terá menos horas de acesso a esse ambiente.
--   Sua sessão no Gitpod expirará após 30 minutos de inatividade e suas alterações serão salvas por até 2 semanas (consulte a próxima seção para reabrir uma sessão expirada).
+- O Gitpod oferece 500 créditos gratuitos por mês, o que equivale a 50 horas de tempo de execução no ambiente de trabalho padrão (até 4 núcleos, 8 GB de RAM e 30 GB de armazenamento).
+- Há também uma opção de ambiente de trabalho que oferece até 8 núcleos, 16 GB de RAM e 50 GB de armazenamento. No entanto, o ambiente de trabalho grande usará seus créditos gratuitos mais rapidamente e você terá menos horas de acesso a esse ambiente.
+- Sua sessão no Gitpod expirará após 30 minutos de inatividade e suas alterações serão salvas por até 2 semanas (consulte a próxima seção para reabrir uma sessão expirada).
 
 Acesse [gitpod.io](https://www.gitpod.io) para mais detalhes.
 
diff --git a/docs/envsetup/01_setup.md b/docs/envsetup/01_setup.md
index 7a740592..820689d2 100644
--- a/docs/envsetup/01_setup.md
+++ b/docs/envsetup/01_setup.md
@@ -38,10 +38,10 @@ After Gitpod has loaded, you should see something similar to the following:
 
 ![Gitpod welcome](img/gitpod.welcome.png)
 
--   **The sidebar** allows you to customize your Gitpod environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository.
--   **The terminal** allows you to run all the programs in the repository. For example, both `nextflow` and `docker` are installed and can be executed.
--   **The file explorer** allows you to view and edit files. Clicking on a file in the explorer will open it within the main window.
--   **The Simple Browser** lets you view the nf-training material browser (<https://training.nextflow.io/>). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`.
+- **The sidebar** allows you to customize your Gitpod environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository.
+- **The terminal** allows you to run all the programs in the repository. For example, both `nextflow` and `docker` are installed and can be executed.
+- **The file explorer** allows you to view and edit files. Clicking on a file in the explorer will open it within the main window.
+- **The Simple Browser** lets you view the nf-training material browser (<https://training.nextflow.io/>). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`.
 
 ### Gitpod resources
 
diff --git a/docs/envsetup/02_local.md b/docs/envsetup/02_local.md
index 6fd6f65d..919d31a2 100644
--- a/docs/envsetup/02_local.md
+++ b/docs/envsetup/02_local.md
@@ -10,18 +10,18 @@ Nextflow can be used on any POSIX-compatible system (Linux, macOS, Windows Subsy
 
 **Requirements**
 
--   Bash
--   [Java 11 (or later, up to 21)](https://www.oracle.com/technetwork/java/javase/downloads/index.html)
--   [Git](https://git-scm.com/)
--   [Docker](https://docs.docker.com/get-docker/)
+- Bash
+- [Java 11 (or later, up to 21)](https://www.oracle.com/technetwork/java/javase/downloads/index.html)
+- [Git](https://git-scm.com/)
+- [Docker](https://docs.docker.com/get-docker/)
 
 **Optional requirements**
 
--   [Singularity](https://github.com/sylabs/singularity) 2.5.x (or later)
--   [Conda](https://conda.io/) 4.5 (or later)
--   [Graphviz](http://www.graphviz.org/)
--   [AWS CLI](https://aws.amazon.com/cli/)
--   A configured AWS Batch computing environment
+- [Singularity](https://github.com/sylabs/singularity) 2.5.x (or later)
+- [Conda](https://conda.io/) 4.5 (or later)
+- [Graphviz](http://www.graphviz.org/)
+- [AWS CLI](https://aws.amazon.com/cli/)
+- A configured AWS Batch computing environment
 
 ## Download Nextflow
 
diff --git a/docs/hands_on/02_workflow.md b/docs/hands_on/02_workflow.md
index ade16e81..e35f5f9d 100644
--- a/docs/hands_on/02_workflow.md
+++ b/docs/hands_on/02_workflow.md
@@ -10,17 +10,17 @@ Variant calling is done **simultaneously** on bam files from **all replicates**.
 
 Documentation for all software used in the workflow can be found at the following links:
 
--   [samtools](http://www.htslib.org/doc/samtools.html)
--   [picard `CreateSequenceDictionary`](https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary)
--   [STAR](http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf)
--   [vcftools](https://vcftools.github.io/man_latest.html)
--   [GATK tools](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/index)
-    -   [`SplitNCigarReads`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_rnaseq_SplitNCigarReads.php)
-    -   [`BaseRecalibrator`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php)
-    -   [`PrintReads`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_readutils_PrintReads.php)
-    -   [`HaplotypeCaller`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php)
-    -   [`VariantFiltration`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php)
-    -   [`ASEReadCounter`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_rnaseq_ASEReadCounter.php)
+- [samtools](http://www.htslib.org/doc/samtools.html)
+- [picard `CreateSequenceDictionary`](https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary)
+- [STAR](http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf)
+- [vcftools](https://vcftools.github.io/man_latest.html)
+- [GATK tools](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/index)
+    - [`SplitNCigarReads`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_rnaseq_SplitNCigarReads.php)
+    - [`BaseRecalibrator`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php)
+    - [`PrintReads`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_readutils_PrintReads.php)
+    - [`HaplotypeCaller`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php)
+    - [`VariantFiltration`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php)
+    - [`ASEReadCounter`](https://software.broadinstitute.org/gatk/gatkdocs/3.6-0/org_broadinstitute_gatk_tools_walkers_rnaseq_ASEReadCounter.php)
 
 ## Pipeline steps
 
@@ -178,9 +178,9 @@ java -jar /usr/gitc/GATK35.jar -T HaplotypeCaller \
 
 Variant filtering is done as recommended in the GATK best practices:
 
--   keep clusters of at least 3 SNPs that are within a window of 35 bases between them
--   estimate strand bias using Fisher’s Exact Test with values > 30.0 (Phred-scaled p-value)
--   use variant call confidence score `QualByDepth` (QD) with values < 2.0. The QD is the QUAL score normalized by allele depth (AD) for a variant.
+- keep clusters of at least 3 SNPs that are within a window of 35 bases between them
+- estimate strand bias using Fisher’s Exact Test with values > 30.0 (Phred-scaled p-value)
+- use variant call confidence score `QualByDepth` (QD) with values < 2.0. The QD is the QUAL score normalized by allele depth (AD) for a variant.
 
 ```bash
 java -jar /usr/gitc/GATK35.jar -T VariantFiltration \
diff --git a/docs/hands_on/04_implementation.md b/docs/hands_on/04_implementation.md
index 2f4b7a9b..c1145544 100644
--- a/docs/hands_on/04_implementation.md
+++ b/docs/hands_on/04_implementation.md
@@ -117,10 +117,10 @@ Now we have our inputs set up we can move onto the processes. In our first proce
 
 The first process has the following structure:
 
--   **Name**: `prepare_genome_samtools`
--   **Command**: create a genome index for the genome fasta with samtools
--   **Input**: the genome fasta file
--   **Output**: the samtools genome index file
+- **Name**: `prepare_genome_samtools`
+- **Command**: create a genome index for the genome fasta with samtools
+- **Input**: the genome fasta file
+- **Output**: the samtools genome index file
 
 !!! exercise "Problem #2"
 
@@ -218,10 +218,10 @@ Our first process created the genome index for GATK using samtools. For the next
 
 The next process should have the following structure:
 
--   **Name**: `prepare_genome_picard`
--   **Command**: create a genome dictionary for the genome fasta with Picard tools
--   **Input**: the genome fasta file
--   **Output**: the genome dictionary file
+- **Name**: `prepare_genome_picard`
+- **Command**: create a genome dictionary for the genome fasta with Picard tools
+- **Input**: the genome fasta file
+- **Output**: the genome dictionary file
 
 !!! exercise "Problem #3"
 
@@ -303,10 +303,10 @@ Next we must create a genome index for the [STAR](https://github.com/alexdobin/S
 
 The next process has the following structure:
 
--   **Name**: `prepare_star_genome_index`
--   **Command**: create a STAR genome index for the genome fasta
--   **Input**: the genome fasta file
--   **Output**: a directory containing the STAR genome index
+- **Name**: `prepare_star_genome_index`
+- **Command**: create a STAR genome index for the genome fasta
+- **Input**: the genome fasta file
+- **Output**: a directory containing the STAR genome index
 
 !!! exercise "Problem #4"
 
@@ -403,12 +403,12 @@ Next on to something a little more tricky. The next process takes two inputs: th
 
 The next process has the following structure:
 
--   **Name**: `prepare_vcf_file`
--   **Command**: create a filtered and recoded set of variants
--   **Input**:
-    -   the variants file
-    -   the blacklisted regions file
--   **Output**: a tuple containing the filtered/recoded VCF file and the tab index (TBI) file.
+- **Name**: `prepare_vcf_file`
+- **Command**: create a filtered and recoded set of variants
+- **Input**:
+    - the variants file
+    - the blacklisted regions file
+- **Output**: a tuple containing the filtered/recoded VCF file and the tab index (TBI) file.
 
 !!! exercise "Problem #5"
 
@@ -524,13 +524,13 @@ In this process, for each sample, we align the reads to our genome using the STA
 
 The process has the following structure:
 
--   **Name**: `rnaseq_mapping_star`
--   **Command**: mapping of the RNA-Seq reads using STAR
--   **Input**:
-    -   the genome fasta file
-    -   the STAR genome index
-    -   a tuple containing the replicate id and paired read files
--   **Output**: a tuple containing replicate id, aligned bam file & aligned bam file index
+- **Name**: `rnaseq_mapping_star`
+- **Command**: mapping of the RNA-Seq reads using STAR
+- **Input**:
+    - the genome fasta file
+    - the STAR genome index
+    - a tuple containing the replicate id and paired read files
+- **Output**: a tuple containing replicate id, aligned bam file & aligned bam file index
 
 !!! Exercise "Problem #6"
 
@@ -725,14 +725,14 @@ The process creates `k+1` new reads (where `k` is the number of `N` cigar elemen
 
 The next process has the following structure:
 
--   **Name**: `rnaseq_gatk_splitNcigar`
--   **Command**: split reads on Ns in CIGAR string using GATK
--   **Input**:
-    -   the genome fasta file
-    -   the genome index made with samtools
-    -   the genome dictionary made with picard
-    -   a tuple containing replicate id, aligned bam file and aligned bam file index from the STAR mapping
--   **Output**: a tuple containing the replicate id, the split bam file and the split bam index file
+- **Name**: `rnaseq_gatk_splitNcigar`
+- **Command**: split reads on Ns in CIGAR string using GATK
+- **Input**:
+    - the genome fasta file
+    - the genome index made with samtools
+    - the genome dictionary made with picard
+    - a tuple containing replicate id, aligned bam file and aligned bam file index from the STAR mapping
+- **Output**: a tuple containing the replicate id, the split bam file and the split bam index file
 
 !!! exercise "Problem #7"
 
@@ -885,15 +885,15 @@ This step uses GATK to detect systematic errors in the base quality scores, sele
 
 The next process has the following structure:
 
--   **Name**: `rnaseq_gatk_recalibrate`
--   **Command**: recalibrate reads from each replicate using GATK
--   **Input**
-    -   the genome fasta file
-    -   the genome index made with samtools
-    -   the genome dictionary made with picard
-    -   a tuple containing replicate id, aligned bam file and aligned bam file index from process 3
-    -   a tuple containing the filtered/recoded VCF file and the tab index (TBI) file from process 1D
--   **Output**: a tuple containing the sample id, the unique bam file and the unique bam index file
+- **Name**: `rnaseq_gatk_recalibrate`
+- **Command**: recalibrate reads from each replicate using GATK
+- **Input**
+    - the genome fasta file
+    - the genome index made with samtools
+    - the genome dictionary made with picard
+    - a tuple containing replicate id, aligned bam file and aligned bam file index from process 3
+    - a tuple containing the filtered/recoded VCF file and the tab index (TBI) file from process 1D
+- **Output**: a tuple containing the sample id, the unique bam file and the unique bam index file
 
 !!! exercise "Problem #8"
 
@@ -1094,14 +1094,14 @@ This steps call variants with GATK HaplotypeCaller. You can find details of the
 
 The next process has the following structure:
 
--   **Name**: `rnaseq_call_variants`
--   **Command**: variant calling of each sample using GATK
--   **Input**:
-    -   the genome fasta file
-    -   the genome index made with samtools
-    -   the genome dictionary made with picard
-    -   a tuple containing replicate id, aligned bam file and aligned bam file index from process 4
--   **Output**: a tuple containing the sample id the resulting variant calling file (vcf)
+- **Name**: `rnaseq_call_variants`
+- **Command**: variant calling of each sample using GATK
+- **Input**:
+    - the genome fasta file
+    - the genome index made with samtools
+    - the genome dictionary made with picard
+    - a tuple containing replicate id, aligned bam file and aligned bam file index from process 4
+- **Output**: a tuple containing the sample id the resulting variant calling file (vcf)
 
 !!! exercise "Problem #9"
 
@@ -1291,20 +1291,20 @@ We must process the VCF result to prepare variants file for allele specific expr
 
 You should implement two processes having the following structure:
 
--   _1st process_
-    -   **Name**: `post_process_vcf`
-    -   **Command**: post-process the variant calling file (vcf) of each sample
-    -   **Input**:
-        -   tuple containing the sample ID and vcf file
-        -   a tuple containing the filtered/recoded VCF file and the tab index (TBI) file from process 1D
-    -   **Output**: a tuple containing the sample id, the variant calling file (vcf) and a file containing common SNPs
--   _2nd process_
-    -   **Name**: `prepare_vcf_for_ase`
-    -   **Command**: prepare the VCF for allele specific expression (ASE) and generate a figure in R.
-    -   **Input**: a tuple containing the sample id, the variant calling file (vcf) and a file containing common SNPs
-    -   **Output**:
-        -   a tuple containing the sample ID and known SNPs in the sample for ASE
-        -   a figure of the SNPs generated in R as a PDF file
+- _1st process_
+    - **Name**: `post_process_vcf`
+    - **Command**: post-process the variant calling file (vcf) of each sample
+    - **Input**:
+        - tuple containing the sample ID and vcf file
+        - a tuple containing the filtered/recoded VCF file and the tab index (TBI) file from process 1D
+    - **Output**: a tuple containing the sample id, the variant calling file (vcf) and a file containing common SNPs
+- _2nd process_
+    - **Name**: `prepare_vcf_for_ase`
+    - **Command**: prepare the VCF for allele specific expression (ASE) and generate a figure in R.
+    - **Input**: a tuple containing the sample id, the variant calling file (vcf) and a file containing common SNPs
+    - **Output**:
+        - a tuple containing the sample ID and known SNPs in the sample for ASE
+        - a figure of the SNPs generated in R as a PDF file
 
 !!! exercise "Problem #10"
 
@@ -1615,14 +1615,14 @@ Now we are ready for the final process.
 
 The next process has the following structure:
 
--   **Name**: `ASE_knownSNPs`
--   **Command**: calculate allele counts at a set of positions with GATK tools
--   **Input**:
-    -   genome fasta file
-    -   genome index file from samtools
-    -   genome dictionary file
-    -   the `grouped_vcf_bam_bai_ch` channel
--   **Output**: the allele specific expression file (`ASE.tsv`)
+- **Name**: `ASE_knownSNPs`
+- **Command**: calculate allele counts at a set of positions with GATK tools
+- **Input**:
+    - genome fasta file
+    - genome index file from samtools
+    - genome dictionary file
+    - the `grouped_vcf_bam_bai_ch` channel
+- **Output**: the allele specific expression file (`ASE.tsv`)
 
 !!! exercise "Problem #12"
 
diff --git a/docs/hello_nextflow/01_orientation.md b/docs/hello_nextflow/01_orientation.md
index 887b3238..99e3dfff 100644
--- a/docs/hello_nextflow/01_orientation.md
+++ b/docs/hello_nextflow/01_orientation.md
@@ -74,19 +74,19 @@ If you run this inside `hello-nextflow`, you should see the following output:
 
 **Here's a summary of what you should know to get started:**
 
--   **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in.
+- **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in.
 
--   **The `hello-*` directories** are directories used in the later Parts of the course where we are working with more than just one workflow file.
+- **The `hello-*` directories** are directories used in the later Parts of the course where we are working with more than just one workflow file.
 
--   **The file `nextflow.config`** is a configuration file that sets minimal environment properties.
-    You can ignore it for now.
+- **The file `nextflow.config`** is a configuration file that sets minimal environment properties.
+  You can ignore it for now.
 
--   **The `data` directory** contains the input data we'll use in most of the course. The dataset is described in detail in Part 3, when we introduce it for the first time.
+- **The `data` directory** contains the input data we'll use in most of the course. The dataset is described in detail in Part 3, when we introduce it for the first time.
 
--   **The `solutions` directory** contains the completed workflow scripts that result from each step of the course.
-    They are intended to be used as a reference to check your work and troubleshoot any issues.
-    The name and number in the filename correspond to the step of the relevant part of the course.
-    For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World.
+- **The `solutions` directory** contains the completed workflow scripts that result from each step of the course.
+  They are intended to be used as a reference to check your work and troubleshoot any issues.
+  The name and number in the filename correspond to the step of the relevant part of the course.
+  For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World.
 
 !!!tip
 
diff --git a/docs/hello_nextflow/01_orientation.pt.md b/docs/hello_nextflow/01_orientation.pt.md
index 826c2c35..59a0d381 100644
--- a/docs/hello_nextflow/01_orientation.pt.md
+++ b/docs/hello_nextflow/01_orientation.pt.md
@@ -69,15 +69,15 @@ Se você executar isso dentro do diretório `hello-nextflow`, verá a seguinte s
 
 **Aqui está um resumo do que você deveria saber para começar:**
 
--   **Os arquivos `.nf`** são _scripts_ de fluxo de trabalho nomeados com base na parte do curso em que são utilizados.
+- **Os arquivos `.nf`** são _scripts_ de fluxo de trabalho nomeados com base na parte do curso em que são utilizados.
 
--   **Os diretórios `hello-*`** são usados nas partes posteriores do curso, onde trabalhamos com mais de um arquivo de fluxo de trabalho.
+- **Os diretórios `hello-*`** são usados nas partes posteriores do curso, onde trabalhamos com mais de um arquivo de fluxo de trabalho.
 
--   **O arquivo `nextflow.config`** é um arquivo de configuração que define propriedades mínimas do ambiente. Você pode ignorá-lo por enquanto.
+- **O arquivo `nextflow.config`** é um arquivo de configuração que define propriedades mínimas do ambiente. Você pode ignorá-lo por enquanto.
 
--   **O diretório `data`** contém os dados de entrada que usaremos na maior parte do curso. O conjunto de dados é descrito em detalhe na Parte 3, quando o introduzimos pela primeira vez.
+- **O diretório `data`** contém os dados de entrada que usaremos na maior parte do curso. O conjunto de dados é descrito em detalhe na Parte 3, quando o introduzimos pela primeira vez.
 
--   **O diretório `solutions`** contém os _scripts_ de fluxo de trabalho completos resultantes de cada etapa do curso. Eles servem como referência para verificar seu trabalho e solucionar quaisquer problemas. As informações de nome e o número presentes no nome do arquivo correspondem à etapa da parte relevante do curso. Por exemplo, o arquivo `hello-world-4.nf` é o resultado esperado ao completar as etapas 1 a 4 da Parte 1: Hello World.
+- **O diretório `solutions`** contém os _scripts_ de fluxo de trabalho completos resultantes de cada etapa do curso. Eles servem como referência para verificar seu trabalho e solucionar quaisquer problemas. As informações de nome e o número presentes no nome do arquivo correspondem à etapa da parte relevante do curso. Por exemplo, o arquivo `hello-world-4.nf` é o resultado esperado ao completar as etapas 1 a 4 da Parte 1: Hello World.
 
 !!!dica
 
diff --git a/docs/hello_nextflow/02_hello_world.md b/docs/hello_nextflow/02_hello_world.md
index eea4fda2..8d6588d0 100644
--- a/docs/hello_nextflow/02_hello_world.md
+++ b/docs/hello_nextflow/02_hello_world.md
@@ -218,12 +218,12 @@ This tells you what is the subdirectory path for that specific process call (som
 
 If we look inside the subdirectory, we find the following log files:
 
--   **`.command.begin`**: Metadata related to the beginning of the execution of the process task
--   **`.command.err`**: Error messages (stderr) emitted by the process task
--   **`.command.log`**: Complete log output emitted by the process task
--   **`.command.out`**: Regular output (stdout) by the process task
--   **`.command.sh`**: The command that was run by the process task call
--   **`.exitcode`**: The exit code resulting from the command
+- **`.command.begin`**: Metadata related to the beginning of the execution of the process task
+- **`.command.err`**: Error messages (stderr) emitted by the process task
+- **`.command.log`**: Complete log output emitted by the process task
+- **`.command.out`**: Regular output (stdout) by the process task
+- **`.command.sh`**: The command that was run by the process task call
+- **`.exitcode`**: The exit code resulting from the command
 
 In this case, you can look for your output in the `.command.out` file, since that's where stdout output is captured.
 If you open it, you'll find the `Hello World!` greeting, which was the expected result of our minimalist workflow.
@@ -400,8 +400,8 @@ Using this mode means Nextflow will only run processes that are either new, have
 
 There are two key advantages to doing this:
 
--   If you're in the middle of developing your pipeline, you can iterate more rapidly since you only effectively have to run the process(es) you're actively working on in order to test your changes.
--   If you're running a pipeline in production and something goes wrong, in many cases you can fix the issue and relaunch the pipeline, and it will resume running from the point of failure, which can save you a lot of time and compute.
+- If you're in the middle of developing your pipeline, you can iterate more rapidly since you only effectively have to run the process(es) you're actively working on in order to test your changes.
+- If you're running a pipeline in production and something goes wrong, in many cases you can fix the issue and relaunch the pipeline, and it will resume running from the point of failure, which can save you a lot of time and compute.
 
 ### 4.1. Run the workflow again with `-resume`
 
diff --git a/docs/hello_nextflow/03_hello_containers.md b/docs/hello_nextflow/03_hello_containers.md
index ecb66184..ec975b17 100644
--- a/docs/hello_nextflow/03_hello_containers.md
+++ b/docs/hello_nextflow/03_hello_containers.md
@@ -417,9 +417,9 @@ Doing these exercises is _not required_ to understand later parts of the trainin
 We have a list of computer and biology pioneers in the `containers/data/pioneers.csv` file.
 At a high level, to complete this exercise you will need to:
 
--   Modify the default `params.input_file` to point to the `pioneers.csv` file.
--   Create a `getQuote` process that uses the `quote` container to fetch a quote for each input.
--   Connect the output of the `getQuote` process to the `cowsay` process to display the quote.
+- Modify the default `params.input_file` to point to the `pioneers.csv` file.
+- Create a `getQuote` process that uses the `quote` container to fetch a quote for each input.
+- Connect the output of the `getQuote` process to the `cowsay` process to display the quote.
 
 For the `quote` container image, you can either use the one you built yourself in the previous stretch exercise or use the one you got from Seqera Containers .
 
diff --git a/docs/hello_nextflow/04_hello_genomics.md b/docs/hello_nextflow/04_hello_genomics.md
index fe495dfa..b1b3e522 100644
--- a/docs/hello_nextflow/04_hello_genomics.md
+++ b/docs/hello_nextflow/04_hello_genomics.md
@@ -40,10 +40,10 @@ So to recap, we're going to develop a workflow that does the following:
 
 ### Dataset
 
--   **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary).
--   **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small slice of data on chromosome 20 to keep the file sizes small.
-    The sequencing data is in (Binary Alignment Map) format, i.e. genome sequencing reads that have already been mapped to the reference genome.
--   **A list of genomic intervals**, i.e. coordinates on the genome where our samples have data suitable for calling variants, provided in BED format.
+- **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary).
+- **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small slice of data on chromosome 20 to keep the file sizes small.
+  The sequencing data is in (Binary Alignment Map) format, i.e. genome sequencing reads that have already been mapped to the reference genome.
+- **A list of genomic intervals**, i.e. coordinates on the genome where our samples have data suitable for calling variants, provided in BED format.
 
 ---
 
diff --git a/docs/hello_nextflow/05_hello_operators.md b/docs/hello_nextflow/05_hello_operators.md
index 35e1e797..946c6640 100644
--- a/docs/hello_nextflow/05_hello_operators.md
+++ b/docs/hello_nextflow/05_hello_operators.md
@@ -39,10 +39,10 @@ So to recap, we're going to develop a workflow that does the following:
 
 ### Dataset
 
--   **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary).
--   **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small portion on chromosome 20 to keep the file sizes small.
-    The sequencing data is in [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) (Binary Alignment Map) format, _i.e._ genome sequencing reads that have already been mapped to the reference genome.
--   **A list of genomic intervals**, _i.e._ coordinates on the genome where our samples have data suitable for calling variants, provided in BED format.
+- **A reference genome** consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and sequence dictionary).
+- **Three whole genome sequencing samples** corresponding to a family trio (mother, father and son), which have been subset to a small portion on chromosome 20 to keep the file sizes small.
+  The sequencing data is in [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) (Binary Alignment Map) format, _i.e._ genome sequencing reads that have already been mapped to the reference genome.
+- **A list of genomic intervals**, _i.e._ coordinates on the genome where our samples have data suitable for calling variants, provided in BED format.
 
 ---
 
@@ -257,8 +257,8 @@ It should look very familiar, but feel free to run it if you want to satisfy you
 
 We're going to start by making two changes:
 
--   Add the `-ERC GVCF` parameter to the GATK HaplotypeCaller command;
--   Update the output file path to use the corresponding `.g.vcf` extension, as per GATK convention.
+- Add the `-ERC GVCF` parameter to the GATK HaplotypeCaller command;
+- Update the output file path to use the corresponding `.g.vcf` extension, as per GATK convention.
 
 Make sure you add a backslash (`\`) at the end of the previous line when you add `-ERC GVCF`.
 
diff --git a/docs/hello_nextflow/06_hello_config.md b/docs/hello_nextflow/06_hello_config.md
index 1b0b85ff..d6f672f9 100644
--- a/docs/hello_nextflow/06_hello_config.md
+++ b/docs/hello_nextflow/06_hello_config.md
@@ -33,10 +33,10 @@ hello-config
 └── nextflow.config
 ```
 
--   **`main.nf`** is a workflow based on `hello-operators.nf`, the workflow produced by completing Part 4 of this training course;
+- **`main.nf`** is a workflow based on `hello-operators.nf`, the workflow produced by completing Part 4 of this training course;
 
--   **`nextflow.config`** is a copy of the original `nextflow.config` file from the `hello-nextflow` directory, one level up (where we've been working so far).
-    Whenever there is a file named `nextflow.config` in the current directory, Nextflow will automatically load configuration from it. The one we have been using contains the following lines:
+- **`nextflow.config`** is a copy of the original `nextflow.config` file from the `hello-nextflow` directory, one level up (where we've been working so far).
+  Whenever there is a file named `nextflow.config` in the current directory, Nextflow will automatically load configuration from it. The one we have been using contains the following lines:
 
     ```console title="nextflow.config" linenums="1"
     docker.fixOwnership = true
@@ -54,8 +54,8 @@ hello-config
 
     Anything you put into the `nextflow.config` can be overridden at runtime by providing the relevant process directives or parameters and values on the command line, or by importing another configuration file, according to the order of precedence described [here](https://www.nextflow.io/docs/latest/config.html).
 
--   **`demo-params.json`** is a parameter file intended for supplying parameter values to a workflow.
-    We will use it in section 5 of this tutorial.
+- **`demo-params.json`** is a parameter file intended for supplying parameter values to a workflow.
+  We will use it in section 5 of this tutorial.
 
 The one thing that's missing is a way to point to the original data without making a copy of it or updating the file paths wherever they're specified.
 The simplest solution is to link to the data location.
@@ -431,12 +431,12 @@ This runs each step on the same machine that Nextflow is running on.
 However, for large workloads, you will typically want to use a distributed executor such as an HPC or cloud.
 Nextflow supports several different distributed executors, including:
 
--   HPC (SLURM, PBS, SGE)
--   AWS Batch
--   Google Batch
--   Azure Batch
--   Kubernetes
--   GA4GH TES
+- HPC (SLURM, PBS, SGE)
+- AWS Batch
+- Google Batch
+- Azure Batch
+- Kubernetes
+- GA4GH TES
 
 The executor is subject to a process directive called `executor`. By default it is set to `local`, so the following configuration is implied:
 
diff --git a/docs/hello_nextflow/08_hello_nf-test.md b/docs/hello_nextflow/08_hello_nf-test.md
index 860286a6..1665d181 100644
--- a/docs/hello_nextflow/08_hello_nf-test.md
+++ b/docs/hello_nextflow/08_hello_nf-test.md
@@ -179,9 +179,9 @@ In plain English, the logic of the test reads as follows:
 
 The expected results are formulated as `assert` statements.
 
--   `assert process.success` states that we expect the process to run successfully and complete without any failures.
--   `snapshot(process.out).match()` states that we expect the result of the run to be identical to the result obtained in a previous run (if applicable).
-    We discuss this in more detail later.
+- `assert process.success` states that we expect the process to run successfully and complete without any failures.
+- `snapshot(process.out).match()` states that we expect the result of the run to be identical to the result obtained in a previous run (if applicable).
+  We discuss this in more detail later.
 
 For most real-world modules (which usually require some kind of input), this is not yet a functional test.
 We need to add the inputs that will be fed to the process, and any parameters if applicable.
@@ -293,9 +293,9 @@ params {
 
 Finally, it's time to run our test! Let's break down the syntax.
 
--   The basic command is `nf-test test`.
--   To that, we add `--profile docker_on` to specify that we want Nextflow to run the test with Docker enabled.
--   Then the test file that we want to run.
+- The basic command is `nf-test test`.
+- To that, we add `--profile docker_on` to specify that we want Nextflow to run the test with Docker enabled.
+- Then the test file that we want to run.
 
 !!!note
 
@@ -345,8 +345,8 @@ If we re-run the test, the program will check that the new output matches the ou
 
 If, in the course of future development, something in the code changes that causes the output to be different, the test will fail and we will have to determine whether the change is expected or not.
 
--   If it turns out that something in the code broke, we will have to fix it, with the expectation that the fixed code will pass the test.
--   If it is an expected change (e.g., the tool has been improved and the results are better) then we will need to update the snapshot to accept the new output as the reference to match, using the parameter `--update-snapshot` when we run the test command.
+- If it turns out that something in the code broke, we will have to fix it, with the expectation that the fixed code will pass the test.
+- If it is an expected change (e.g., the tool has been improved and the results are better) then we will need to update the snapshot to accept the new output as the reference to match, using the parameter `--update-snapshot` when we run the test command.
 
 ### 1.7. Add more tests to `SAMTOOLS_INDEX`
 
@@ -460,8 +460,8 @@ Now that we know how to handle the simplest case, we're going to kick things up
 As the second step in our pipeline, its input depends on the output of another process.
 We can deal with this in two ways:
 
--   Manually generate some static test data that is suitable as intermediate input to the process;
--   Use a special [setup method](https://www.nf-test.com/docs/testcases/setup/) to handle it dynamically for us.
+- Manually generate some static test data that is suitable as intermediate input to the process;
+- Use a special [setup method](https://www.nf-test.com/docs/testcases/setup/) to handle it dynamically for us.
 
 **Spoiler:** We're going to use the setup method.
 
diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md
index cfc032f7..0f8b0186 100644
--- a/docs/hello_nextflow/09_hello_nf-core.md
+++ b/docs/hello_nextflow/09_hello_nf-core.md
@@ -18,12 +18,12 @@ The nf-core collection currently offers [over 100 pipelines](https://nf-co.re/pi
 
 Each released pipeline has a dedicated page that includes 6 documentation sections:
 
--   **Introduction:** An introduction and overview of the pipeline
--   **Usage:** Descriptions of how to execute the pipeline
--   **Parameters:** Grouped pipeline parameters with descriptions
--   **Output:** Descriptions and examples of the expected output files
--   **Results:** Example output files generated from the full test dataset
--   **Releases & Statistics:** Pipeline version history and statistics
+- **Introduction:** An introduction and overview of the pipeline
+- **Usage:** Descriptions of how to execute the pipeline
+- **Parameters:** Grouped pipeline parameters with descriptions
+- **Output:** Descriptions and examples of the expected output files
+- **Results:** Example output files generated from the full test dataset
+- **Releases & Statistics:** Pipeline version history and statistics
 
 You should read the pipeline documentation carefully to understand what a given pipeline does and how it can be configured before attempting to run it.
 
@@ -384,8 +384,8 @@ The nf-core pipeline template has a `main.nf` script that calls `myfirstpipeline
 
 Instead of having one large monolithic pipeline script, it's broken up into smaller script components, namely, modules and subworkflows:
 
--   **Modules:** Wrappers around a single process
--   **Subworkflows:** Two or more modules that are packaged together as a mini workflow
+- **Modules:** Wrappers around a single process
+- **Subworkflows:** Two or more modules that are packaged together as a mini workflow
 
 <figure class="excalidraw">
     --8<-- "docs/hello_nextflow/img/nested.excalidraw.svg"
@@ -442,10 +442,10 @@ In the template, the `nextflow.config` file is a central configuration file and
 
 There are several configuration files that are stored in the `conf` folder and are added to the configuration by default or optionally as profiles:
 
--   `base.config`: A 'blank slate' config file, appropriate for general use on most high-performance computing environments. This defines broad bins of resource usage, for example, which are convenient to apply to modules.
--   `modules.config`: Additional module directives and arguments.
--   `test.config`: A profile to run the pipeline with minimal test data.
--   `test_full.config`: A profile to run the pipeline with a full-sized test dataset.
+- `base.config`: A 'blank slate' config file, appropriate for general use on most high-performance computing environments. This defines broad bins of resource usage, for example, which are convenient to apply to modules.
+- `modules.config`: Additional module directives and arguments.
+- `test.config`: A profile to run the pipeline with minimal test data.
+- `test_full.config`: A profile to run the pipeline with a full-sized test dataset.
 
 #### `nextflow_schema.json`
 
@@ -642,8 +642,8 @@ Using this module information you can work out what inputs are required for the
 
 1.  `tuple val(meta), path(reads)`
 
-    -   A tuple with a meta _map_ and a list of FASTQ _files_
-    -   The channel `ch_samplesheet` used by the `FASTQC` process can be used as the reads input.
+    - A tuple with a meta _map_ and a list of FASTQ _files_
+    - The channel `ch_samplesheet` used by the `FASTQC` process can be used as the reads input.
 
 Only one input channel is required, and it already exists, so it can be added to your `firstpipeline.nf` file without any additional channel creation or modifications.
 
@@ -1009,9 +1009,9 @@ In the next step we will take a look how we can add a new key to the `meta` map
 
 nf-core pipelines typically use samplesheets as inputs to the pipelines. This allows us to:
 
--   validate each entry and print specific error messages.
--   attach information to each input file.
--   track which datasets are processed.
+- validate each entry and print specific error messages.
+- attach information to each input file.
+- track which datasets are processed.
 
 Samplesheets are comma-separated text files with a header row specifying the column names, followed by one entry per row. For example, the samplesheet that we have been using during this teaching module looks like this:
 
diff --git a/docs/hello_nextflow/index.md b/docs/hello_nextflow/index.md
index eb625e07..02797df1 100644
--- a/docs/hello_nextflow/index.md
+++ b/docs/hello_nextflow/index.md
@@ -22,11 +22,11 @@ In this workshop, you will learn foundational concepts for building pipelines.
 
 By the end of this workshop you will be able to:
 
--   Describe and utilize core Nextflow components sufficient to build a simple multi-step workflow
--   Describe next-step concepts such as operators and channel factories
--   Launch a Nextflow workflow locally
--   Find and interpret outputs (results) and log files generated by Nextflow
--   Troubleshoot basic issues
+- Describe and utilize core Nextflow components sufficient to build a simple multi-step workflow
+- Describe next-step concepts such as operators and channel factories
+- Launch a Nextflow workflow locally
+- Find and interpret outputs (results) and log files generated by Nextflow
+- Troubleshoot basic issues
 
 ## Audience & prerequisites
 
@@ -34,5 +34,5 @@ This is a workshop for those who are completely new to Nextflow. Some basic fami
 
 **Prerequisites**
 
--   A GitHub account
--   Experience with command line
+- A GitHub account
+- Experience with command line
diff --git a/docs/hello_nextflow/index.pt.md b/docs/hello_nextflow/index.pt.md
index c9704696..ce116674 100644
--- a/docs/hello_nextflow/index.pt.md
+++ b/docs/hello_nextflow/index.pt.md
@@ -22,11 +22,11 @@ Neste workshop, você aprenderá conceitos fundamentais para a construção de p
 
 Ao final deste workshop você será capaz de:
 
--   Descrever e utilizar os principais componentes do Nextflow o suficiente para criar um fluxo de trabalho simples de várias etapas
--   Descrever conceitos como operadores e fábricas de canal
--   Lançar um fluxo de trabalho localmente com Nextflow
--   Encontrar e interpretar saídas (resultados) e arquivos de log gerados pelo Nextflow
--   Solucionar problemas básicos
+- Descrever e utilizar os principais componentes do Nextflow o suficiente para criar um fluxo de trabalho simples de várias etapas
+- Descrever conceitos como operadores e fábricas de canal
+- Lançar um fluxo de trabalho localmente com Nextflow
+- Encontrar e interpretar saídas (resultados) e arquivos de log gerados pelo Nextflow
+- Solucionar problemas básicos
 
 ## Público e pré-requisitos
 
@@ -34,5 +34,5 @@ Este é um workshop para aqueles que são completamente novos no Nextflow. Algum
 
 **Pré-requisitos**
 
--   Uma conta GitHub
--   Experiência com linha de comando
+- Uma conta GitHub
+- Experiência com linha de comando
diff --git a/docs/hello_nextflow/seqera/01_run_with_cli.md b/docs/hello_nextflow/seqera/01_run_with_cli.md
index d9a321db..f2e4349c 100644
--- a/docs/hello_nextflow/seqera/01_run_with_cli.md
+++ b/docs/hello_nextflow/seqera/01_run_with_cli.md
@@ -147,9 +147,9 @@ If you ran your pipeline from the `hello_nextflow` directory, you'll see somethi
 
 Notice that configuration for our pipeline run is being run pulled from three separate files:
 
--   `/home/gitpod/.nextflow/config` - This is the global configuration file we just added.
--   `/home/gitpod/.nextflow/assets/nextflow-io/hello/nextflow.config` - This is the `nextflow.config` file from the `nextflow-io/hello` repository.
--   `/workspace/gitpod/nf-training/hello-nextflow/nextflow.config` - This is the `nextflow.config` file from our current working directory.
+- `/home/gitpod/.nextflow/config` - This is the global configuration file we just added.
+- `/home/gitpod/.nextflow/assets/nextflow-io/hello/nextflow.config` - This is the `nextflow.config` file from the `nextflow-io/hello` repository.
+- `/workspace/gitpod/nf-training/hello-nextflow/nextflow.config` - This is the `nextflow.config` file from our current working directory.
 
 Nextflow resolves these configurations at runtime with a [specific order of precedence](https://www.nextflow.io/docs/latest/config.html#configuration-file).
 The general rule, however, is that more specific configurations override less specific ones, and config/params specified on the CLI will override defaults in the config files.
@@ -160,10 +160,10 @@ Helpfully, Seqera Platform shows us the final output of this configuration resol
 
 You have learned how to:
 
--   Set up your Seqera Platform token by exporting it to your environment.
--   Run Nextflow CLI with Seqera Platform visualizing and capturing logs.
--   Set up Seqera Platform logging by default.
--   Use Seqera Platform to explore the resolved configuration of a Nextflow pipeline.
+- Set up your Seqera Platform token by exporting it to your environment.
+- Run Nextflow CLI with Seqera Platform visualizing and capturing logs.
+- Set up Seqera Platform logging by default.
+- Use Seqera Platform to explore the resolved configuration of a Nextflow pipeline.
 
 ### What's next?
 
diff --git a/docs/hello_nextflow/seqera/02_run_with_launchpad.md b/docs/hello_nextflow/seqera/02_run_with_launchpad.md
index c3080d72..4b2f41fb 100644
--- a/docs/hello_nextflow/seqera/02_run_with_launchpad.md
+++ b/docs/hello_nextflow/seqera/02_run_with_launchpad.md
@@ -75,10 +75,10 @@ Click on the task to see the task details:
 
 You have learned how to:
 
--   Switch between organizations and workspaces in Seqera Platform.
--   Launch a Nextflow pipeline that ran in the cloud using Seqera Platform.
--   Monitor the progress of the pipeline run.
--   Inspect the details of a task that was executed as part of the pipeline.
+- Switch between organizations and workspaces in Seqera Platform.
+- Launch a Nextflow pipeline that ran in the cloud using Seqera Platform.
+- Monitor the progress of the pipeline run.
+- Inspect the details of a task that was executed as part of the pipeline.
 
 ### Next steps
 
diff --git a/docs/help.fr.md b/docs/help.fr.md
index fffc4677..2d1c88ae 100644
--- a/docs/help.fr.md
+++ b/docs/help.fr.md
@@ -13,8 +13,8 @@ Notre formidable communauté est l'une des grandes forces de Nextflow !
 
 Il existe deux instances Slack :
 
--   Nextflow ([register here](https://www.nextflow.io/slack-invite.html))
--   nf-core ([register here](https://nf-co.re/join/slack))
+- Nextflow ([register here](https://www.nextflow.io/slack-invite.html))
+- nf-core ([register here](https://nf-co.re/join/slack))
 
 En général, le slack Nextflow est le meilleur car il s'adresse à l'ensemble de la communauté.
 La seule exception est si vous suivez la formation dans le cadre d'un atelier organisé par nf-core, auquel cas on vous aura indiqué où poser vos questions.
diff --git a/docs/help.pt.md b/docs/help.pt.md
index e7fe13bb..a6190c35 100644
--- a/docs/help.pt.md
+++ b/docs/help.pt.md
@@ -13,8 +13,8 @@ Nossa incrível comunidade é um dos grandes pontos fortes do Nextflow!
 
 Existem duas instâncias relevantes do Slack:
 
--   Nextflow ([inscreva-se aqui](https://www.nextflow.io/slack-invite.html))
--   nf-core ([inscreva-se aqui](https://nf-co.re/join/slack))
+- Nextflow ([inscreva-se aqui](https://www.nextflow.io/slack-invite.html))
+- nf-core ([inscreva-se aqui](https://nf-co.re/join/slack))
 
 Geralmente, o Slack do Nextflow é melhor, pois atende a toda a comunidade.
 A exceção é se você estiver seguindo o treinamento através de um workshop organizado pelo projeto nf-core. Nesse caso, você deve ter sido informado sobre onde fazer perguntas.
diff --git a/docs/index.md b/docs/index.md
index 16c530e3..8ef2b901 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -15,9 +15,9 @@ We have several distinct training courses available on this website. Scroll down
 
 The training courses listed below are designed to be useable as a self-service resource; you can work through them on your own at any time (see Environment Setup for practical details). However, you may get even more out of them by joining a group training event.
 
--   Free online events are run regularly by the nf-core community, see the [nf-core events page](https://nf-co.re/events) for more.
--   Seqera (the company that develops Nextflow) runs a variety of training events, see the [Seqera Events](https://seqera.io/events/) page and look for 'Seqera Sessions' and 'Nextflow Summit'.
--   Our Community team also regularly teaches trainings hosted by third party organizations; announcements and signups for those are typically managed by the third-party hosts.
+- Free online events are run regularly by the nf-core community, see the [nf-core events page](https://nf-co.re/events) for more.
+- Seqera (the company that develops Nextflow) runs a variety of training events, see the [Seqera Events](https://seqera.io/events/) page and look for 'Seqera Sessions' and 'Nextflow Summit'.
+- Our Community team also regularly teaches trainings hosted by third party organizations; announcements and signups for those are typically managed by the third-party hosts.
 
 When you're ready to get down to work, click on the 'Open in Gitpod' button, either on this page or on the index page of the course you chose, to open a web-based training environment (requires a free GitHub account).
 
diff --git a/docs/index.pt.md b/docs/index.pt.md
index e301ad23..72286bfe 100644
--- a/docs/index.pt.md
+++ b/docs/index.pt.md
@@ -15,9 +15,9 @@ Temos vários treinamentos distintos disponíveis neste site. Role para baixo pa
 
 Os treinamentos listados abaixo foram construídos de modo que você possa fazê-los de forma independente; você pode trabalhar neles sozinho a qualquer momento (veja Configuração do Ambiente para detalhes práticos). No entanto, você pode usufruir ainda mais desses materiais ao participar de um evento de treinamento em grupo.
 
--   Eventos online gratuitos são realizados regularmente pela comunidade nf-core, veja a [página de eventos nf-core](https://nf-co.re/events) para mais informações.
--   A Seqera (a empresa que desenvolve o Nextflow) realiza uma variedade de eventos de treinamento. Veja a página [Seqera Events](https://seqera.io/events/) e procure por 'Seqera Sessions' e 'Nextflow Summit'.
--   Nosso time de Comunidade também ministra regularmente treinamentos hospedados por outras organizações; anúncios e inscrições para eles são normalmente gerenciados por essas organizações.
+- Eventos online gratuitos são realizados regularmente pela comunidade nf-core, veja a [página de eventos nf-core](https://nf-co.re/events) para mais informações.
+- A Seqera (a empresa que desenvolve o Nextflow) realiza uma variedade de eventos de treinamento. Veja a página [Seqera Events](https://seqera.io/events/) e procure por 'Seqera Sessions' e 'Nextflow Summit'.
+- Nosso time de Comunidade também ministra regularmente treinamentos hospedados por outras organizações; anúncios e inscrições para eles são normalmente gerenciados por essas organizações.
 
 Quando decidir começar o treinamento, clique no botão 'Abrir no Gitpod', nesta página ou na página de índice do treinamento escolhido, para abrir um ambiente de treinamento dentro do seu próporio navegador (requer uma conta gratuita no GitHub).
 
diff --git a/docs/nf_customize/02_nf-core.md b/docs/nf_customize/02_nf-core.md
index bc9802b8..00fe254c 100644
--- a/docs/nf_customize/02_nf-core.md
+++ b/docs/nf_customize/02_nf-core.md
@@ -10,18 +10,18 @@ One of the key benefits of nf-core is that it promotes open development, testing
 
 **Key Features of nf-core pipelines**
 
--   **Documentation**
-    -   nf-core pipelines have extensive documentation covering installation, usage, and description of output files to ensure that you won't be left in the dark.
--   **CI Testing**
-    -   Every time a change is made to the pipeline code, nf-core pipelines use continuous-integration testing to ensure that nothing has broken.
--   **Stable Releases**
-    -   nf-core pipelines use GitHub releases to tag stable versions of the code and software, making pipeline runs totally reproducible.
--   **Packaged software**
-    -   Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda, or other software management tools. There is no need for any software installations.
--   **Portable and reproducible**
-    -   nf-core pipelines follow best practices to ensure maximum portability and reproducibility. The large community makes the pipelines exceptionally well-tested and easy to execute.
--   **Cloud-ready**
-    -   nf-core pipelines are tested on AWS after every major release. You can even browse results live on the website and use outputs for your own benchmarking.
+- **Documentation**
+    - nf-core pipelines have extensive documentation covering installation, usage, and description of output files to ensure that you won't be left in the dark.
+- **CI Testing**
+    - Every time a change is made to the pipeline code, nf-core pipelines use continuous-integration testing to ensure that nothing has broken.
+- **Stable Releases**
+    - nf-core pipelines use GitHub releases to tag stable versions of the code and software, making pipeline runs totally reproducible.
+- **Packaged software**
+    - Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda, or other software management tools. There is no need for any software installations.
+- **Portable and reproducible**
+    - nf-core pipelines follow best practices to ensure maximum portability and reproducibility. The large community makes the pipelines exceptionally well-tested and easy to execute.
+- **Cloud-ready**
+    - nf-core pipelines are tested on AWS after every major release. You can even browse results live on the website and use outputs for your own benchmarking.
 
 nf-core is published in Nature Biotechnology: [Nat Biotechnol 38, 276–278 (2020). Nature Biotechnology](https://www.nature.com/articles/s41587-020-0439-x). An updated preprint is available at [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.05.10.592912v1).
 
@@ -35,12 +35,12 @@ The [nf-core website](https://nf-co.re/) hosts a full list of pipelines, as well
 
 Each released pipeline has a dedicated page that includes 6 documentation sections:
 
--   **Introduction:** An introduction and overview of the pipeline
--   **Usage:** Descriptions of how to execute the pipeline
--   **Parameters:** Grouped pipeline parameters with descriptions
--   **Output:** Descriptions and examples of the expected output files
--   **Results:** Example output files generated from the full test dataset
--   **Releases & Statistics:** Pipeline version history and statistics
+- **Introduction:** An introduction and overview of the pipeline
+- **Usage:** Descriptions of how to execute the pipeline
+- **Parameters:** Grouped pipeline parameters with descriptions
+- **Output:** Descriptions and examples of the expected output files
+- **Results:** Example output files generated from the full test dataset
+- **Releases & Statistics:** Pipeline version history and statistics
 
 Each section should be explored by a user to understand what the pipeline does and how it can be configured.
 
diff --git a/docs/nf_customize/03_execution.md b/docs/nf_customize/03_execution.md
index fef005d2..de693327 100644
--- a/docs/nf_customize/03_execution.md
+++ b/docs/nf_customize/03_execution.md
@@ -10,25 +10,25 @@ It was created using the full nf-core template and is designed to run and config
 
 The [`nf-core/demo`](https://nf-co.re/demo/) pipeline consists of three processes:
 
--   ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)): Read quality control
--   ([`SEQTK_TRIM`](https://github.com/lh3/seqtk)): Trim low quality bases from FASTQ files
--   ([`MULTIQC`](http://multiqc.info/)): Present quality control reports for raw reads
+- ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)): Read quality control
+- ([`SEQTK_TRIM`](https://github.com/lh3/seqtk)): Trim low quality bases from FASTQ files
+- ([`MULTIQC`](http://multiqc.info/)): Present quality control reports for raw reads
 
 [`nf-core/demo`](https://nf-co.re/demo/) takes a samplesheet that contains paths to FASTQ files as an input and will produce four output folders with logs and reports:
 
--   `fastqc/`
-    -   `*_fastqc.html`: FastQC report containing quality metrics.
-    -   `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
--   `fq/`
-    -   `*.fastp.html`: Trimmed fq files.
--   `multiqc/`
-    -   `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-    -   `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-    -   `multiqc_plots/`: directory containing static images from the report in various formats.
--   `pipeline_info/`
-    -   Reports generated by Nextflow
-    -   Reports generated by nf-core
-    -   Parameters file
+- `fastqc/`
+    - `*_fastqc.html`: FastQC report containing quality metrics.
+    - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+- `fq/`
+    - `*.fastp.html`: Trimmed fq files.
+- `multiqc/`
+    - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+    - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+    - `multiqc_plots/`: directory containing static images from the report in various formats.
+- `pipeline_info/`
+    - Reports generated by Nextflow
+    - Reports generated by nf-core
+    - Parameters file
 
 You can view the code for this pipeline on the [`nf-core/demo` GitHub repository](https://github.com/nf-core/demo).
 
diff --git a/docs/nf_customize/04_config.md b/docs/nf_customize/04_config.md
index 6a0d156f..1eaafe7e 100644
--- a/docs/nf_customize/04_config.md
+++ b/docs/nf_customize/04_config.md
@@ -56,24 +56,24 @@ All parameters have a default configuration that is defined using the `nextflow.
 
 There are also several `includeConfig` statements in the `nextflow.config` file that are used to include additional `.config` files from the `conf/` folder. Each additional `.config` file contains categorized configuration information for your pipeline execution, some of which can be optionally included:
 
--   `base.config`
-    -   Included by the pipeline by default.
-    -   Generous resource allocations using labels.
-    -   Does not specify any method for software management and expects software to be available (or specified elsewhere).
--   `igenomes.config`
-    -   Included by the pipeline by default.
-    -   Default configuration to access reference files stored on [AWS iGenomes](https://ewels.github.io/AWS-iGenomes/).
--   `igenomes_ignored.config`
-    -   Empty genomes dictionary to use when igenomes is ignored.
--   `modules.config`
-    -   Included by the pipeline by default.
-    -   Module-specific configuration options (both mandatory and optional).
--   `test.config`
-    -   Only included if specified as a profile.
-    -   A configuration profile to test the pipeline with a small test dataset.
--   `test_full.config`
-    -   Only included if specified as a profile.
-    -   A configuration profile to test the pipeline with a full-size test dataset.
+- `base.config`
+    - Included by the pipeline by default.
+    - Generous resource allocations using labels.
+    - Does not specify any method for software management and expects software to be available (or specified elsewhere).
+- `igenomes.config`
+    - Included by the pipeline by default.
+    - Default configuration to access reference files stored on [AWS iGenomes](https://ewels.github.io/AWS-iGenomes/).
+- `igenomes_ignored.config`
+    - Empty genomes dictionary to use when igenomes is ignored.
+- `modules.config`
+    - Included by the pipeline by default.
+    - Module-specific configuration options (both mandatory and optional).
+- `test.config`
+    - Only included if specified as a profile.
+    - A configuration profile to test the pipeline with a small test dataset.
+- `test_full.config`
+    - Only included if specified as a profile.
+    - A configuration profile to test the pipeline with a full-size test dataset.
 
 !!! note
 
@@ -81,10 +81,10 @@ There are also several `includeConfig` statements in the `nextflow.config` file
 
 Profiles used by nf-core pipelines can be broadly categorized into two groups:
 
--   **Software management profiles**
-    -   Profiles for the management of software using software management tools, for example, `docker`, `singularity`, and `conda`.
--   **Test profiles**
-    -   Profiles to execute the pipeline with a standardized set of test data and parameters, for example, `test` and `test_full`.
+- **Software management profiles**
+    - Profiles for the management of software using software management tools, for example, `docker`, `singularity`, and `conda`.
+- **Test profiles**
+    - Profiles to execute the pipeline with a standardized set of test data and parameters, for example, `test` and `test_full`.
 
 nf-core pipelines are required to define software containers and environments that can be activated using profiles. Although it is possible to run the pipelines with software installed by other methods (e.g., environment modules or manual installation), using Docker or Singularity is more sharable, convenient, and reproducible.
 
@@ -100,11 +100,11 @@ For shared resources such as an HPC cluster, you may consider developing a share
 
 Nextflow will also look for files that are external to the pipeline project directory. These files include:
 
--   The config file `$HOME/.nextflow/config`
--   A config file named `nextflow.config` in your current directory
--   Custom files specified using the command line
-    -   A parameter file that is provided using the `-params-file` option
-    -   A config file that are provided using the `-c` option
+- The config file `$HOME/.nextflow/config`
+- A config file named `nextflow.config` in your current directory
+- Custom files specified using the command line
+    - A parameter file that is provided using the `-params-file` option
+    - A config file that are provided using the `-c` option
 
 **You do not need to use all of these files to run your pipeline.**
 
diff --git a/docs/nf_customize/05_tools.md b/docs/nf_customize/05_tools.md
index d8d0c6dd..82ff170e 100644
--- a/docs/nf_customize/05_tools.md
+++ b/docs/nf_customize/05_tools.md
@@ -101,15 +101,15 @@ nf-core pipelines download
 
 The download tool will interactively prompt you for the required information is no arguments are supplied. Each prompt option has a flag and if all flags are supplied then it will run without a request for any additional user input:
 
--   **Pipeline name**
-    -   Name of pipeline you would like to download.
--   **Pipeline revision**
-    -   The revision you would like to download.
--   **Pull containers**
-    -   If you would like to download Singularity images.
-    -   The path to a folder where you would like to store these images if you have not set your `NXF_SINGULARITY_CACHEDIR`.
--   **Choose compression type**
-    -   The compression type for Singularity images.
+- **Pipeline name**
+    - Name of pipeline you would like to download.
+- **Pipeline revision**
+    - The revision you would like to download.
+- **Pull containers**
+    - If you would like to download Singularity images.
+    - The path to a folder where you would like to store these images if you have not set your `NXF_SINGULARITY_CACHEDIR`.
+- **Choose compression type**
+    - The compression type for Singularity images.
 
 Alternatively, you could build your own execution command with the command line options.
 
diff --git a/docs/nf_customize/index.md b/docs/nf_customize/index.md
index 4e2e30aa..66c0a354 100644
--- a/docs/nf_customize/index.md
+++ b/docs/nf_customize/index.md
@@ -14,9 +14,9 @@ Let's get started!
 
 By the end of this workshop you will be able to:
 
--   Discuss the ways an nf-core pipeline can be customized
--   Identify the files and code contributing to the default pipeline configuration
--   Utilize nf-core tooling to list, launch, and download pipelines
+- Discuss the ways an nf-core pipeline can be customized
+- Identify the files and code contributing to the default pipeline configuration
+- Utilize nf-core tooling to list, launch, and download pipelines
 
 ## Audience & prerequisites
 
@@ -24,6 +24,6 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 
 **Prerequisites**
 
--   A GitHub account
--   Experience with command line
--   Experience writing pipelines with Nextflow
+- A GitHub account
+- Experience with command line
+- Experience writing pipelines with Nextflow
diff --git a/docs/nf_develop/1_02_create.md b/docs/nf_develop/1_02_create.md
index 449282cc..1eb1ccc7 100644
--- a/docs/nf_develop/1_02_create.md
+++ b/docs/nf_develop/1_02_create.md
@@ -156,8 +156,8 @@ The nf-core pipeline template has a `main.nf` script that calls `myfirstpipeline
 
 Instead of having one large monolithic pipeline script, it's broken up into smaller script components, namely, modules and subworkflows:
 
--   **Modules:** Wrappers around a single process
--   **Subworkflows:** Two or more modules that are packaged together as a mini workflow
+- **Modules:** Wrappers around a single process
+- **Subworkflows:** Two or more modules that are packaged together as a mini workflow
 
 <figure class="excalidraw">
 --8<-- "docs/nf_develop/img/nested.excalidraw.svg"
@@ -215,12 +215,12 @@ In the template, the `nextflow.config` file is a central configuration file and
 
 There are several configuration files that are stored in the `conf` folder and are added to the configuration by default or optionally as profiles:
 
--   `base.config`: A 'blank slate' config file, appropriate for general use on most high performance compute environments.
--   `igenomes.config`: Defines reference genomes using iGenome paths.
--   `igenomes_ignored.config`: Empty genomes dictionary to use when igenomes is ignored
--   `modules.config`: Additional module directives and arguments.
--   `test.config`: A profile to run the pipeline with minimal test data.
--   `test_full.config`: A profile to run the pipeline with a full-sized test dataset.
+- `base.config`: A 'blank slate' config file, appropriate for general use on most high performance compute environments.
+- `igenomes.config`: Defines reference genomes using iGenome paths.
+- `igenomes_ignored.config`: Empty genomes dictionary to use when igenomes is ignored
+- `modules.config`: Additional module directives and arguments.
+- `test.config`: A profile to run the pipeline with minimal test data.
+- `test_full.config`: A profile to run the pipeline with a full-sized test dataset.
 
 ### `.nf-core.yml`
 
@@ -282,14 +282,14 @@ Automated workflows are an important part of the nf-core pipeline template.
 
 By default, the template comes with several automated tests that utilize GitHub Actions, each of which are configured in the `.github/workflows` folder:
 
--   `branch.yml`: Sets the branch protection for the nf-core repository
--   `ci.yml`: Run small pipeline tests with the small test datasets
--   `clean-up.yml`: Automated testing for stale and closed GitHub issues and PRs in the nf-core repo
--   `download_pipeline.yml`: Test a pipeline download with `nf-core pipelines download`.
--   `fix-linting.yml`: Fix linting by adding a comment to a PR
--   `linting_comment.yml`: Triggered after the linting action and posts an automated comment to the PR, even if the PR is coming from a fork
--   `linting.yml`: Triggered on pushes and PRs to the repository and runs `nf-core pipelines lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
--   `release-announcements.yml`: Automatic release toot and tweet announcements for nf-core pipeline releases
+- `branch.yml`: Sets the branch protection for the nf-core repository
+- `ci.yml`: Run small pipeline tests with the small test datasets
+- `clean-up.yml`: Automated testing for stale and closed GitHub issues and PRs in the nf-core repo
+- `download_pipeline.yml`: Test a pipeline download with `nf-core pipelines download`.
+- `fix-linting.yml`: Fix linting by adding a comment to a PR
+- `linting_comment.yml`: Triggered after the linting action and posts an automated comment to the PR, even if the PR is coming from a fork
+- `linting.yml`: Triggered on pushes and PRs to the repository and runs `nf-core pipelines lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+- `release-announcements.yml`: Automatic release toot and tweet announcements for nf-core pipeline releases
 
 Many of these tests are only configured for the nf-core repo. However, they can be modified for your repository or ignored if they are superfluous to your requirements.
 
diff --git a/docs/nf_develop/1_03_pipeline.md b/docs/nf_develop/1_03_pipeline.md
index 2b286ee6..787247ce 100644
--- a/docs/nf_develop/1_03_pipeline.md
+++ b/docs/nf_develop/1_03_pipeline.md
@@ -2,8 +2,8 @@
 
 The nf-core pipeline template is a working pipeline and comes pre-configured with two modules:
 
--   [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/): A tool that performs quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses that can be used to give a quick impression of your data.
--   [MultiQC](https://multiqc.info/): A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/): A tool that performs quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses that can be used to give a quick impression of your data.
+- [MultiQC](https://multiqc.info/): A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
 
 !!! note "Pre-configured modules are optional"
 
@@ -181,8 +181,8 @@ Using this module information you can work out what inputs are required for the
 
 1.  `tuple val(meta), path(reads)`
 
-    -   A tuple with a meta _map_ and a list of FASTQ _files_
-    -   The channel `ch_samplesheet` used by the `FASTQC` process can be used as the reads input.
+    - A tuple with a meta _map_ and a list of FASTQ _files_
+    - The channel `ch_samplesheet` used by the `FASTQC` process can be used as the reads input.
 
 As only one input channel required, and it already exists, it can be added to your `mypipeline.nf` file without any additional channel creation or modifications.
 
diff --git a/docs/nf_develop/extra.md b/docs/nf_develop/extra.md
index cd320533..9e10eda1 100644
--- a/docs/nf_develop/extra.md
+++ b/docs/nf_develop/extra.md
@@ -2,11 +2,11 @@ In Part 2 of this workshop, you will use the nf-core tooling to continue develop
 
 By the end of this workshop you will be able to:
 
--   Add local modules
--   Patch nf-core modules
--   Customize linting tests
--   Sync TEMPLATE
--   Bump versions
+- Add local modules
+- Patch nf-core modules
+- Customize linting tests
+- Sync TEMPLATE
+- Bump versions
 
 # Customizing the template
 
@@ -122,8 +122,8 @@ As an individual or group, you may want to keep your own library of modules and/
 
 The nf-core modules command comes with two flags for specifying a custom remote:
 
--   `--git-remote <git remote url>`: Specifies the repository from which the modules should be fetched as a git URL.
--   `--branch <branch name>`: Specifies the branch from which the modules should be fetched.
+- `--git-remote <git remote url>`: Specifies the repository from which the modules should be fetched as a git URL.
+- `--branch <branch name>`: Specifies the branch from which the modules should be fetched.
 
 Note that a custom remote must follow a similar directory structure to that of `nf-core/modules` for the nf-core commands to work properly.
 
@@ -198,9 +198,9 @@ Having a universal way of versioning the development projects is the best way to
 
 For example, starting with a release version `1.4.3`, bumping the version to:
 
--   `1.4.4` would be a patch release for minor things such as fixing bugs.
--   `1.5` would be a minor release, for example adding some new features.
--   `2.0` would correspond to the major release where results would no longer be backward compatible.
+- `1.4.4` would be a patch release for minor things such as fixing bugs.
+- `1.5` would be a minor release, for example adding some new features.
+- `2.0` would correspond to the major release where results would no longer be backward compatible.
 
 The pipeline version number is mentioned in a lot of different places in nf-core pipelines. The `nf-core bump-version` command updates the version for you automatically, so that you don't accidentally miss any. It can be used for each pipeline release, and again for the next development version after release.
 
diff --git a/docs/nf_develop/index.md b/docs/nf_develop/index.md
index 20522ade..6ee82bac 100644
--- a/docs/nf_develop/index.md
+++ b/docs/nf_develop/index.md
@@ -16,10 +16,10 @@ In this workshop, you will utilize the nf-core tooling to build a small pipeline
 
 By the end of this workshop you will be able to:
 
--   Discuss the benefits of using the nf-core pipeline template
--   Identify the features of nf-core pipeline template that enable best practices
--   Add nf-core modules to a pipeline using the nf-core tooling
--   Add parameters to a pipeline and update the schema using the nf-core tooling
+- Discuss the benefits of using the nf-core pipeline template
+- Identify the features of nf-core pipeline template that enable best practices
+- Add nf-core modules to a pipeline using the nf-core tooling
+- Add parameters to a pipeline and update the schema using the nf-core tooling
 
 ## Audience & prerequisites
 
@@ -27,6 +27,6 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 
 **Prerequisites**
 
--   A GitHub account
--   Experience with command line
--   Experience writing pipelines with Nextflow
+- A GitHub account
+- Experience with command line
+- Experience writing pipelines with Nextflow
diff --git a/docs/troubleshoot/01_orientation.md b/docs/troubleshoot/01_orientation.md
index 885a6e1e..81351583 100644
--- a/docs/troubleshoot/01_orientation.md
+++ b/docs/troubleshoot/01_orientation.md
@@ -22,6 +22,6 @@ To check everything is working as expected you can run the `hello-gatk.nf` scrip
 
 If all of the data has been copied and unzipped correctly you should see the pipeline execute three processes:
 
--   `SAMTOOLS_INDEX`
--   `GATK_HAPLOTYPECALLER`
--   `GATK_JOINTGENOTYPING`
+- `SAMTOOLS_INDEX`
+- `GATK_HAPLOTYPECALLER`
+- `GATK_JOINTGENOTYPING`
diff --git a/docs/troubleshoot/index.md b/docs/troubleshoot/index.md
index ecb56b52..45d69e73 100644
--- a/docs/troubleshoot/index.md
+++ b/docs/troubleshoot/index.md
@@ -14,9 +14,9 @@ In this workshop, you will utilize the `hello-gatk.nf` script created for the [H
 
 By the end of this workshop you will be able to:
 
--   Describe Nextflow error outputs
--   List common causes of pipeline errors
--   Troubleshoot basic pipeline errors
+- Describe Nextflow error outputs
+- List common causes of pipeline errors
+- Troubleshoot basic pipeline errors
 
 ## Audience & prerequisites
 
@@ -24,6 +24,6 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 
 **Prerequisites**
 
--   A GitHub account
--   Experience with command line
--   Experience writing pipelines with Nextflow
+- A GitHub account
+- Experience with command line
+- Experience writing pipelines with Nextflow