millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-09-20 23:32:05 +00:00
Code Issues Releases Packages Activity

Merge pull request #139 from nf-core/testing-docs

Browse source 
Add documentation for Testing
This commit is contained in:
Harshil Patel 2021-02-07 22:35:01 +00:00 committed by GitHub
commit dcabde6b85
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 27 additions and 14 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

41
README.md
View file

@ -124,16 +124,16 @@ We have added a directory called [`software/SOFTWARE/TOOL/`](software/SOFTWARE/T
```console
.
├── software
│   ├── SOFTWARE
│   │   └── TOOL
│   │   ├── functions.nf ## Utility functions imported in main module script
│   │   ├── main.nf ## Main module script
│   │   ├── meta.yml ## Documentation for module, input, output, params, author
│   │   └── test
│   │   ├── input ## Soft-link input test data from "tests/"
│   │   ├── main.nf ## Minimal workflow to test module
│   │   ├── nextflow.config ## Minimal config to test module
│   │   └── output ## Upload output files from test for unit testing
│   └── SOFTWARE
│      └── TOOL
│      ├── functions.nf ## Utility functions imported in main module script
│      ├── main.nf ## Main module script
│      └── meta.yml ## Documentation for module, input, output, params, author
├── test
│   └── SOFTWARE
│      └── TOOL
│   ├── main.nf ## Minimal workflow to test module
│   └── test.yml ## Pytest-workflow test file
```
### Guidelines
@ -228,15 +228,28 @@ We also use a standardised parameter called `params.publish_dir_mode` that can b
- Test files MUST be kept as tiny as possible.
- Every module MUST be tested by adding a test workflow with a toy dataset in the [`test/`](software/fastqc/test) directory of the module.
- Every module MUST be tested by adding a test workflow with a toy dataset in the [`tests/`](tests/software/fastqc/main.nf) directory of the module.
- Generic files from [`tests/data/`](tests/data/) MUST be reused by symlinking them into the [`test/input/`](software/fastqc/test/input/) directory of the module.
- Generic files from [`tests/data/`](tests/data/) MUST be reused by importing them as `file(${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz)`
- Any outputs produced by the test workflow MUST be placed in a folder called [`test/output/`](software/fastqc/test/output/) so that they can be used for unit testing.
- Any outputs produced by the test workflow MUST be included in the [pytest-workflow](https://pytest-workflow.readthedocs.io/en/stable) for that tool. md5sum is preferred, however it's acceptable to not have it on files that the hash changes due to various headers and timestamps (html). Please do your best to avoid just checking for the file being present.
- If the appropriate test data doesn't exist for your module then it MUST be added to [`tests/data/`](tests/data/).
- A GitHub Actions workflow file MUST be added to [`.github/workflows/`](.github/workflows/) e.g. [`.github/workflows/fastqc.yml`](.github/workflows/fastqc.yml).
- A filter for the module must be created in [`.github/filters.yml`](.github/filters.yml). Please include any paths specific for that tool or upstream of that tool (For example bowtie build is upstream of bowtie align).
#### Running Tests Locally
0. Have either `docker`, `singularity` or `conda` installed
1. See [pytest-workflow installation](https://pytest-workflow.readthedocs.io/en/stable/#installation) for directions to install
2. Run
``` bash
PROFILE=docker pytest --tag new_module --symlink --wt 2 --kwdof
PROFILE=conda pytest --tag new_module --symlink --wt 2 --kwdof
TMPDIR=~ PROFILE=singularity pytest --tag new_module --symlink --wt 2 --kwdof
alias nf-test="PROFILE=docker pytest --tag new_module --symlink --wt 2 --kwdof"
```
### Documentation