A python package with helper tools for the nf-core community.
Install the package with the following command:
pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
Alternatively, if you would like to edit the files locally:
# You should probably specify your fork instead
git clone https://github.com/nf-core/tools.git nf-core-tools
cd nf-core-tools
python setup.py develop
# Or with pip
pip install -e .
The lint
subcommand checks a given pipeline for all nf-core community guidelines.
This is the same test that is used on the automated continuous integration tests.
For example, the current version looks something like this:
$ cd path/to/my_pipeline
$ nf-core lint .
INFO:root:Checking required files exist
INFO:root:Checking pipeline config variables
INFO:root:
=================
LINTING RESULTS
=================
10 tests passed
1 tests had warnings
1 tests failed
Warnings:
https://nf-core.github.io/errors#1: File not found: tests/run_test.sh
Failures:
https://nf-core.github.io/errors#1: File not found: LICENSE
INFO:root:Sorry, some tests failed - exiting with a non-zero error code...