convert console snippets to bash snippets in the template

CHANGELOG.md

@@ -11,6 +11,7 @@
 - Add Gitpod and Mamba profiles to the pipeline template ([#1673](https://github.com/nf-core/tools/pull/1673))
 - Remove call to `getGenomeAttribute` in `main.nf` when running `nf-core create` without iGenomes ([#1670](https://github.com/nf-core/tools/issues/1670))
 - Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
+- Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729))
 
 ### Linting
 

nf_core/pipeline-template/README.md

@@ -52,7 +52,7 @@ The results obtained from the full-sized test can be viewed on the [nf-core webs
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```console
+   ```bash
    nextflow run {{ name }} -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 
@@ -67,7 +67,7 @@ The results obtained from the full-sized test can be viewed on the [nf-core webs
 
    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
-   ```console
+   ```bash
    nextflow run {{ name }} --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 

nf_core/pipeline-template/docs/usage.md

@@ -16,7 +16,7 @@
 
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
 
-```console
+```bash
 --input '[path to samplesheet file]'
 ```
 
@@ -60,15 +60,15 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 
 The typical command for running the pipeline is as follows:
 
-```console
+```bash
 nextflow run {{ name }} --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
 
 Note that the pipeline will create the following files in your working directory:
 
-```console
+```bash
 work                # Directory containing the nextflow working files
 <OUTDIR>            # Finished results in specified location (defined with --outdir)
 .nextflow_log       # Log file from Nextflow
@@ -79,7 +79,7 @@ work                # Directory containing the nextflow working files
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
-```console
+```bash
 nextflow pull {{ name }}
 ```
 
@@ -262,6 +262,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```console
+```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```