diff --git a/.editorconfig-checker.json b/.ecrc similarity index 86% rename from .editorconfig-checker.json rename to .ecrc index 5724fe8..0fd6191 100644 --- a/.editorconfig-checker.json +++ b/.ecrc @@ -1,10 +1,10 @@ { - "Verbose": true, + "Verbose": false, "Debug": false, "IgnoreDefaults": false, "SpacesAftertabs": false, "NoColor": false, - "Exclude": ["^tests/.runs/", "^\\.nf-test/", "^\\.venv/", "^\\node_modules/", "\\.nf-test.log$"], + "Exclude": ["^tests/.runs/", "^\\.nf-test/", "^\\.venv/", "^\\node_modules/", "\\.nf-test.log$","^\\.git/"], "AllowedContentTypes": [], "PassedFiles": [], "Disable": { diff --git a/README.md b/README.md index c18f030..56408d8 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,20 @@ primary focus of the library is to provide pre-built processes and processing se technologies and made easily available to pipeline's developers through the `nf-core` framework. +# WHY ? `nf-neuro` + +**Let's say you develop a pipeline for neuroimaging**. You want to make it the more _efficient,_ +_reliable, reproducible_ and also be able to _evaluate it_ and _control the quality_ of its outputs. +That's what `nf-neuro` provides to you, **all in one repository**, hosting **all dependencies** you +need to start developing and analyzing. + +The only thing we ask of you is to develop in `Nextflow DSL2`. We use principle and standards +closely aligned with [nf-core](), but we'll make you adapt to them slowly as you go (we still +haven't finished complying to all of them ourselves). Using `nf-neuro` helps accelerate +development in **neuroimaging** and produces better research outcomes for all ! + +--- + - [Using modules from `nf-neuro`](#using-modules-from-nf-neuro) - [Developing in `nf-neuro`](#developing-in-nf-neuro) - [Manual configuration](#manual-configuration) @@ -38,6 +52,7 @@ framework. - [Edit `tests/main.nf.test`](./docs/MODULE.md#edit-testsmainnftest) - [Edit `tests/nextflow.config`](./docs/MODULE.md#edit-testsnextflowconfig) - [Generate tests snapshots](./docs/MODULE.md#generate-tests-snapshots) + - [Request for more test resources](./docs/MODULE.md#request-for-more-test-resources) - [Lint your code](./docs/MODULE.md#lint-your-code) - [Submit your PR](./docs/MODULE.md#submit-your-pr) - [Defining optional input parameters](./docs/MODULE.md#defining-optional-input-parameters) @@ -57,6 +72,8 @@ framework. - [Configuring Docker for easy usage](#configuring-docker-for-easy-usage) - [Installing Prettier and editorconfig](#installing-prettier-and-editorconfig) +--- + # Using modules from `nf-neuro` To import modules from `nf-neuro`, you first need to install [nf-core](https://github.com/nf-core/tools) diff --git a/docs/MODULE.md b/docs/MODULE.md index eea609b..a903a1f 100755 --- a/docs/MODULE.md +++ b/docs/MODULE.md @@ -10,6 +10,7 @@ - [Edit `tests/main.nf.test`](#edit-testsmainnftest) - [Edit `tests/nextflow.config`](#edit-testsnextflowconfig) - [Generate tests snapshots](#generate-tests-snapshots) + - [Request for more test resources](#request-for-more-test-resources) - [Lint your code](#lint-your-code) - [Submit your PR](#submit-your-pr) - [Defining optional input parameters](#defining-optional-input-parameters) @@ -295,7 +296,7 @@ Make sure there is no more comments generated by the `nf-core` template, and you The `nextflow.config` file does not exist by default, so you will have to create it if needed. This is not mandatory, except if you have defined optional parameters with `task.ext` and want to alter their values for some test cases. Refer to [this section](#defining-optional-input-parameters) to see how to scope those parameters to specific tests using `selectors`. -### Generate tests snapshots +## Generate tests snapshots > [!WARNING] > Verify you are located at the root of `nf-neuro` (not inside modules) before @@ -315,7 +316,7 @@ smoothly, look at the snapshot file produced at `tests/main.nf.test.snap` in you directory and validate that ALL outputs produced by test cases are caught. Their `md5sum` is critical to ensure future executions of your test produce valid outputs. -### Request for more test resources +## Request for more test resources Test runners are tailored to restrain their resources usage to specifically what is asked for by Nextflow through the configuration files. For `nf-neuro` tests, you can find this configuration in