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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| repos: | ||
| - repo: https://github.com/psf/black | ||
| rev: 22.3.0 | ||
| hooks: | ||
| - id: black | ||
| language_version: python3.10 | ||
| - repo: https://github.com/pycqa/isort | ||
| rev: 5.10.1 | ||
| hooks: | ||
| - id: isort | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v2.6.2" | ||
| hooks: | ||
| - id: prettier | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: "v4.3.0" | ||
| hooks: | ||
| - id: name-tests-test | ||
| args: [--pytest-test-first] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,7 +2,8 @@ | |
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| [](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster) | ||
| [](https://codecov.io/gh/nf-core/tools) | ||
| [](https://github.com/psf/black) | ||
| [](https://github.com/psf/black) | ||
| [](https://github.com/prettier/prettier) | ||
| [](https://pycqa.github.io/isort/) | ||
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| [](https://bioconda.github.io/recipes/nf-core/README.html) | ||
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@@ -910,42 +911,29 @@ The nf-core DSL2 modules repository is at <https://github.com/nf-core/modules> | |
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| The modules supercommand comes with two flags for specifying a custom remote: | ||
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| - `--github-repository <github repo>`: Specify the repository from which the modules should be fetched. Defaults to `nf-core/modules`. | ||
| - `--branch <branch name>`: Specify the branch from which the modules shoudl be fetched. Defaults to `master`. | ||
| - `--git-remote <git remote url>`: Specify the repository from which the modules should be fetched as a git URL. Defaults to the github repository of `nf-core/modules`. | ||
| - `--branch <branch name>`: Specify the branch from which the modules should be fetched. Defaults to the default branch of your repository. | ||
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| Note that a custom remote must follow a similar directory structure to that of `nf-core/moduleś` for the `nf-core modules` commands to work properly. | ||
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| ### Private remote modules | ||
| For example, if you want to install the `fastqc` module from the repository `nf-core/modules-test` hosted at `gitlab.com`, you can use the following command: | ||
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| In order to get access to your private modules repo, you need to create | ||
| the `~/.config/gh/hosts.yml` file, which is the same file required by | ||
| [GitHub CLI](https://cli.github.com/) to deal with private repositories. | ||
| Such file is structured as follow: | ||
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| ```conf | ||
| github.com: | ||
| oauth_token: <your github access token> | ||
| user: <your github user> | ||
| git_protocol: <ssh or https are valid choices> | ||
| ```terminal | ||
| nf-core modules --git-remote [email protected]:nf-core/modules-test.git install fastqc | ||
| ``` | ||
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| The easiest way to create this configuration file is through _GitHub CLI_: follow | ||
| its [installation instructions](https://cli.github.com/manual/installation) | ||
| and then call: | ||
| Note that a custom remote must follow a similar directory structure to that of `nf-core/moduleś` for the `nf-core modules` commands to work properly. | ||
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| The modules commands will during initalisation try to pull changes from the remote repositories. If you want to disable this, for example | ||
| due to performance reason or if you want to run the commands offline, you can use the flag `--no-pull`. Note however that the commands will | ||
| still need to clone repositories that have previously not been used. | ||
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| ```bash | ||
| gh auth login | ||
| ``` | ||
| ### Private remote repositories | ||
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| After that, you will be able to list and install your private modules without | ||
| providing your github credentials through command line, by using `--github-repository` | ||
| and `--branch` options properly. | ||
| See the documentation on [gh auth login](https://cli.github.com/manual/gh_auth_login>) | ||
| to get more information. | ||
| You can use the modules command with private remote repositories. Make sure that your local `git` is correctly configured with your private remote | ||
| and then specify the remote the same way you would do with a public remote repository. | ||
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| ### List modules | ||
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| The `nf-core modules list` command provides the subcommands `remote` and `local` for listing modules installed in a remote repository and in the local pipeline respectively. Both subcommands come with the `--key <keywords>` option for filtering the modules by keywords. | ||
| The `nf-core modules list` command provides the subcommands `remote` and `local` for listing modules installed in a remote repository and in the local pipeline respectively. Both subcommands allow to use a pattern for filtering the modules by keywords eg: `nf-core modules list <subcommand> <keyword>`. | ||
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| #### List remote modules | ||
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@@ -1078,7 +1066,7 @@ There are three additional flags that you can use when installing a module: | |
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| - `--force`: Overwrite a previously installed version of the module. | ||
| - `--prompt`: Select the module version using a cli prompt. | ||
| - `--sha <commit_sha>`: Install the module at a specific commit from the `nf-core/modules` repository. | ||
| - `--sha <commit_sha>`: Install the module at a specific commit. | ||
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| ### Update modules in a pipeline | ||
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