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docs: Update README with minor edits
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README.md
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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
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- [Adding a new module file](#adding-a-new-module-file)
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- [Module template](#module-template)
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- [Guidelines](#guidelines)
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- [CI tests](#ci-tests)
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- [Testing](#testing)
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- [Documentation](#documentation)
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- [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
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- [Terminology](#terminology)
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@ -131,8 +131,9 @@ We have added a directory called [`software/TOOL/SUBTOOL/`](software/TOOL/SUBTOO
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│ ├── main.nf ## Main module script
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│ └── meta.yml ## Documentation for module, input, output, params, author
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├── tests
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│ └── TOOL
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│ └── SUBTOOL
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│ └── software
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│ └── TOOL
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│ └── SUBTOOL
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│ ├── main.nf ## Minimal workflow to test module
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│ └── test.yml ## Pytest-workflow test file
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```
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@ -240,7 +241,7 @@ The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/fu
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We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`).
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### CI tests
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### Testing
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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.
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@ -281,14 +282,14 @@ In order to test that each module added to `nf-core/modules` is actually working
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```console
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cd /path/to/git/clone/of/nf-core/modules/
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TMPDIR=~ PROFILE=singularity pytest --tag tests/software/bowtie/build --symlink --wt 2 --keep-workflow-wd
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TMPDIR=~ PROFILE=singularity pytest --tag star --symlink --wt 2 --keep-workflow-wd
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```
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- Typical command with Conda:
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```console
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cd /path/to/git/clone/of/nf-core/modules/
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PROFILE=conda pytest --tag tests/software/bowtie/build --symlink --wt 2 --keep-workflow-wd
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PROFILE=conda pytest --tag star --tag star_align_paired_end --symlink --wt 2 --keep-workflow-wd
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```
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### Documentation
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