From 054942bd64e5d86f216ac7a4f71ef0f683f8bec9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 19 Dec 2023 16:05:51 +0100 Subject: [PATCH] fix admonitions --- README.md | 39 ++++++++++++----------------- nf_core/pipeline-template/README.md | 15 ++++------- 2 files changed, 21 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index 1efc968d2d..ec58d668bd 100644 --- a/README.md +++ b/README.md @@ -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 ` \ `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 ` \ `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 @@ -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 ` 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 @@ -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).