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Merge pull request #2591 from mashehu/fix-admonitions
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fix admonitions
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@mashehu
mashehu authored Dec 19, 2023
2 parents 15ddfb4 + 054942b commit 26e43b5
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39 changes: 16 additions & 23 deletions README.md
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Expand Up @@ -225,14 +225,12 @@ Auto-completion for the `nf-core` command is available for bash, zsh and fish. T

After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.

:::note
The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
:::
> [!NOTE]
> The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
> You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
:::info
If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
:::
> [!TIP]
> If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
## Listing pipelines

Expand Down Expand Up @@ -363,18 +361,16 @@ You can run the pipeline by simply providing the directory path for the `workflo
nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results # usual parameters here
```

:::note
If you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
:::
> [!NOTE]
> If you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
### Downloaded nf-core configs

The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.
So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs).

:::warning
This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
:::
> [!WARNING]
> This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
### Downloading Apptainer containers

Expand Down Expand Up @@ -432,18 +428,16 @@ If the download speeds are much slower than your internet connection is capable

Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.

:::tip
Also without access to Tower, pipelines downloaded with the `--tower` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
:::
> [!TIP]
> Also without access to Tower, pipelines downloaded with the `--tower` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
## Pipeline software licences

Sometimes it's useful to see the software licences of the tools used in a pipeline.
You can use the `licences` subcommand to fetch and print the software licence from each conda / PyPI package used in an nf-core pipeline.

:::warning
This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
:::
> [!WARNING]
> This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
<!-- RICH-CODEX
timeout: 10
Expand Down Expand Up @@ -471,10 +465,9 @@ You can then continue to edit, commit and push normally as you build your pipeli

Please see the [nf-core documentation](https://nf-co.re/developers/adding_pipelines) for a full walkthrough of how to create a new nf-core workflow.

:::tip
As the log output says, remember to come and discuss your idea for a pipeline as early as possible!
See the [documentation](https://nf-co.re/developers/adding_pipelines#join-the-community) for instructions.
:::
> [!TIP]
> As the log output says, remember to come and discuss your idea for a pipeline as early as possible!
> See the [documentation](https://nf-co.re/developers/adding_pipelines#join-the-community) for instructions.
Note that if the required arguments for `nf-core create` are not given, it will interactively prompt for them. If you prefer, you can supply them as command line arguments. See `nf-core create --help` for more information.

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15 changes: 5 additions & 10 deletions nf_core/pipeline-template/README.md
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Expand Up @@ -43,11 +43,8 @@

## Usage

:::note
If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
with `-profile test` before running the workflow on actual data.
:::
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
Explain what rows and columns represent. For instance (please edit as appropriate):
Expand Down Expand Up @@ -76,11 +73,9 @@ nextflow run {{ name }} \
--outdir <OUTDIR>
```

:::warning
Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
:::
> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
{% if branded -%}

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