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docs: Update README with minor edits

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Edmund Miller 2021-02-08 19:46:42 -06:00
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README.md
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@ -22,7 +22,7 @@ A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl
- [Adding a new module file](#adding-a-new-module-file) - [Adding a new module file](#adding-a-new-module-file)
- [Module template](#module-template) - [Module template](#module-template)
- [Guidelines](#guidelines) - [Guidelines](#guidelines)
- [CI tests](#ci-tests) - [Testing](#testing)
- [Documentation](#documentation) - [Documentation](#documentation)
- [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules) - [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
- [Terminology](#terminology) - [Terminology](#terminology)
@ -131,10 +131,11 @@ We have added a directory called [`software/TOOL/SUBTOOL/`](software/TOOL/SUBTOO
│      ├── main.nf ## Main module script │      ├── main.nf ## Main module script
│      └── meta.yml ## Documentation for module, input, output, params, author │      └── meta.yml ## Documentation for module, input, output, params, author
├── tests ├── tests
│   └── TOOL │   └── software
│      └── SUBTOOL │    └── TOOL
│   ├── main.nf ## Minimal workflow to test module │       └── SUBTOOL
│   └── test.yml ## Pytest-workflow test file │   ├── main.nf ## Minimal workflow to test module
│   └── test.yml ## Pytest-workflow test file
``` ```
### Guidelines ### Guidelines
@ -240,7 +241,7 @@ The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/fu
We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`). We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`).
### CI tests ### Testing
In order to test that each module added to `nf-core/modules` is actually working and to be able to track any changes to results files between module updates we have set-up a number of Github Actions CI tests to run each module on a minimal test dataset using Docker, Singularity and Conda. In order to test that each module added to `nf-core/modules` is actually working and to be able to track any changes to results files between module updates we have set-up a number of Github Actions CI tests to run each module on a minimal test dataset using Docker, Singularity and Conda.
@ -281,14 +282,14 @@ In order to test that each module added to `nf-core/modules` is actually working
```console ```console
cd /path/to/git/clone/of/nf-core/modules/ cd /path/to/git/clone/of/nf-core/modules/
TMPDIR=~ PROFILE=singularity pytest --tag tests/software/bowtie/build --symlink --wt 2 --keep-workflow-wd TMPDIR=~ PROFILE=singularity pytest --tag star --symlink --wt 2 --keep-workflow-wd
``` ```
- Typical command with Conda: - Typical command with Conda:
```console ```console
cd /path/to/git/clone/of/nf-core/modules/ cd /path/to/git/clone/of/nf-core/modules/
PROFILE=conda pytest --tag tests/software/bowtie/build --symlink --wt 2 --keep-workflow-wd PROFILE=conda pytest --tag star --tag star_align_paired_end --symlink --wt 2 --keep-workflow-wd
``` ```
### Documentation ### Documentation