Merge pull request #485 from nextflow-io/last_min_touches

last min touches

Author: mribeirodantas

docs/advanced/configuration.md

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

docs/advanced/index.md

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

docs/advanced/introduction.md

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

docs/advanced/metadata.md

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

docs/advanced/support.md

@@ -3,6 +3,6 @@ title: Support
 description: Advanced Nextflow Training Workshop
 ---
 
--   Nextflow official documentation is available at [www.nextflow.io/docs/latest](https://www.nextflow.io/docs/latest/)
--   If you have questions, ask on the Seqera Community Forum at [http://community.seqera.io/](http://community.seqera.io/)
--   If you want to chat about Nextflow or plugin development, check the Nextflow Slack at [https://www.nextflow.io/slack-invite.html](https://www.nextflow.io/slack-invite.html)
+- Nextflow official documentation is available at [www.nextflow.io/docs/latest](https://www.nextflow.io/docs/latest/)
+- If you have questions, ask on the Seqera Community Forum at [http://community.seqera.io/](http://community.seqera.io/)
+- If you want to chat about Nextflow or plugin development, check the Nextflow Slack at [https://www.nextflow.io/slack-invite.html](https://www.nextflow.io/slack-invite.html)

docs/basic_training/cache_and_resume.fr.md

@@ -90,9 +90,9 @@ nextflow run <script> -w /some/scratch/dir
 
 Le code de hachage des fichiers d'entrée est calculé en utilisant :
 
--   le chemin d'accès complet au fichier
--   la taille du fichier
--   l'horodatage de la dernière modification
+- le chemin d'accès complet au fichier
+- la taille du fichier
+- l'horodatage de la dernière modification
 
 Par conséquent, le simple fait de ** toucher** un fichier invalidera l'exécution de la tâche correspondante.
 

docs/basic_training/cache_and_resume.md

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

docs/basic_training/cache_and_resume.pt.md

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

docs/basic_training/channels.md

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

docs/basic_training/channels.pt.md

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