From 72cff7a337b0c077f3bfa479172dfb9574f98c34 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 8 Sep 2022 11:22:12 +0200 Subject: [PATCH 1/5] improve template customisation documentation --- README.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 32d0d8f557..7a66557952 100644 --- a/README.md +++ b/README.md @@ -401,7 +401,7 @@ Both options allow you to specify a custom pipeline prefix, as well as selecting The interactive prompts will guide you through the pipeline creation process. An example of a `template.yml` file is shown below. ```yaml -name: cool-pipe +name: coolpipe description: A cool pipeline author: me prefix: cool-pipes-company @@ -413,7 +413,12 @@ skip: - nf_core_configs ``` -This will create a pipeline called `cool-pipe` in the directory `cool-pipes-company-cool-pipe` with `me` as the author. It will exclude all files required for GitHub hosting of the pipeline, the GitHub CI from the pipeline, remove GitHub badges from the `README.md` file, remove pipeline options related to iGenomes and exclude `nf_core/configs` options. +This will create a pipeline called `coolpipe` in the directory `cool-pipes-company-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template: +- `github`: removed all files required for GitHub hosting of the pipeline. Specifically the `.github` folder and `.gitignore` file. +- `ci`: removes the GitHub continuous integration tests from the pipeline. Specifically the `.github/workflows/` folder. +- `github_badges`: removes GitHub badges from the `README.md` file. +- `igenomes`: removes pipeline options related to iGenomes. Including the `conf/igenomes.config` file and all references to it. +- `nf_core_configs`: excludes `nf_core/configs` repository options, which make multiple config profiles for various institutional clusters available. To run the pipeline creation silently (i.e. without any prompts) with the nf-core template, you can use the `--plain` option. From 6b6931aa0019ccc4a03a915fdbf452c518076981 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 8 Sep 2022 11:27:53 +0200 Subject: [PATCH 2/5] explain prefix and update CHANGELOG --- CHANGELOG.md | 1 + README.md | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ee1a97beb..5d3c4ea103 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ - Add `actions/upload-artifact` step to the awstest workflows, to expose the debug log file - Bioconda incompatible conda channel setups now result in more informative error messages ([#1812](https://github.com/nf-core/tools/pull/1812)) +- Improve template customisation documentation ([#1821](https://github.com/nf-core/tools/pull/1821)) ### Linting diff --git a/README.md b/README.md index 7a66557952..5ca789c0b8 100644 --- a/README.md +++ b/README.md @@ -397,7 +397,7 @@ Note that if the required arguments for `nf-core create` are not given, it will The `nf-core create` command comes with a number of options that allow you to customize the creation of a pipeline if you intend to not publish it as an nf-core pipeline. This can be done in two ways: by using interactive prompts, or by supplying a `template.yml` file using the `--template-yaml ` option. -Both options allow you to specify a custom pipeline prefix, as well as selecting parts of the template to be excluded during pipeline creation. +Both options allow you to specify a custom pipeline prefix to use instead of the common `nf-core`, as well as selecting parts of the template to be excluded during pipeline creation. The interactive prompts will guide you through the pipeline creation process. An example of a `template.yml` file is shown below. ```yaml From 5911070686b10a4a59c2b5c44565e28e15d0a22b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 8 Sep 2022 09:30:02 +0000 Subject: [PATCH 3/5] [automated] Fix linting with Prettier --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 5ca789c0b8..d89ba6086b 100644 --- a/README.md +++ b/README.md @@ -414,6 +414,7 @@ skip: ``` This will create a pipeline called `coolpipe` in the directory `cool-pipes-company-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template: + - `github`: removed all files required for GitHub hosting of the pipeline. Specifically the `.github` folder and `.gitignore` file. - `ci`: removes the GitHub continuous integration tests from the pipeline. Specifically the `.github/workflows/` folder. - `github_badges`: removes GitHub badges from the `README.md` file. From 2b00567fd5fd9d9aea932036e1bed1f41d0c5087 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 21 Sep 2022 09:08:59 +0200 Subject: [PATCH 4/5] Update README.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d89ba6086b..d0baab91eb 100644 --- a/README.md +++ b/README.md @@ -415,8 +415,8 @@ skip: This will create a pipeline called `coolpipe` in the directory `cool-pipes-company-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template: -- `github`: removed all files required for GitHub hosting of the pipeline. Specifically the `.github` folder and `.gitignore` file. -- `ci`: removes the GitHub continuous integration tests from the pipeline. Specifically the `.github/workflows/` folder. +- `github`: removed all files required for GitHub hosting of the pipeline. Specifically, the `.github` folder and `.gitignore` file. +- `ci`: removes the GitHub continuous integration tests from the pipeline. Specifically, the `.github/workflows/` folder. - `github_badges`: removes GitHub badges from the `README.md` file. - `igenomes`: removes pipeline options related to iGenomes. Including the `conf/igenomes.config` file and all references to it. - `nf_core_configs`: excludes `nf_core/configs` repository options, which make multiple config profiles for various institutional clusters available. From 81192538b182119074108c039c033a13fb7f2c2e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 17 Oct 2022 15:54:20 +0200 Subject: [PATCH 5/5] Apply suggestions from code review --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c3aaaeccd7..d139286ebe 100644 --- a/README.md +++ b/README.md @@ -421,7 +421,7 @@ The interactive prompts will guide you through the pipeline creation process. An name: coolpipe description: A cool pipeline author: me -prefix: cool-pipes-company +prefix: myorg skip: - github - ci @@ -430,7 +430,7 @@ skip: - nf_core_configs ``` -This will create a pipeline called `coolpipe` in the directory `cool-pipes-company-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template: +This will create a pipeline called `coolpipe` in the directory `myorg-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template: - `github`: removed all files required for GitHub hosting of the pipeline. Specifically, the `.github` folder and `.gitignore` file. - `ci`: removes the GitHub continuous integration tests from the pipeline. Specifically, the `.github/workflows/` folder.