From 184b8e1c32ec7bdd4c6894227762d2577bca1a4e Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 23 Oct 2024 16:40:07 +0200 Subject: [PATCH] remove github style admonitions from tools docs --- .../content/docs/nf-core-tools/installation.md | 14 ++++++++------ .../docs/nf-core-tools/pipelines/download.md | 16 ++++++++++------ 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/sites/docs/src/content/docs/nf-core-tools/installation.md b/sites/docs/src/content/docs/nf-core-tools/installation.md index 7bf73778b7..291c328fa4 100644 --- a/sites/docs/src/content/docs/nf-core-tools/installation.md +++ b/sites/docs/src/content/docs/nf-core-tools/installation.md @@ -168,9 +168,11 @@ 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. - -> [!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. +:::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. +::: + +:::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. +::: diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md index 16536d2c0b..086daeb81f 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md @@ -35,16 +35,18 @@ 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 [Seqera Platform](#adapting-downloads-to-seqera-platform) because the application manages all configurations separately. +:::warning +This option is not available when downloading a pipeline for use with [Seqera Platform](#adapting-downloads-to-seqera-platform) because the application manages all configurations separately. +::: ## Downloading Apptainer containers @@ -102,5 +104,7 @@ 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 _Seqera Platform_ using the `file:/` prefix. -> [!TIP] -> Also without access to Seqera Platform, pipelines downloaded with the `--platform` 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 Seqera Platform, pipelines downloaded with the `--platform` 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. +:::