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nf-core
Python package with helper tools for the nf-core community.
This replaces https://github.com/nf-core/modules/pull/1246 at the reques of @ewels It adds a dynamically-created section to MultiQC, via a MultiQC YAML containing HTML, with a pipeline developer recommended text that users could...
Running `nf-core modules info` never recreates the modules.json. So, if it is out-of-date, the suggested help message is not useful. I think explicitly stating a command is more useful here.
### Description of feature The warning about an unexpected parameters is almost immediately followed by the whole pipeline header about used parameters etc. often leading to it being too fast...
### Description of the bug The `shutil.copytree` argument [`dirs_exist_ok`](https://docs.python.org/3/library/shutil.html#shutil.copytree) is only available in Python version 3.8+ but nf-core tool still support Python 3.7 https://github.com/nf-core/tools/blob/b5400d84d307343353b6ab09aad204231f74fb0e/nf_core/modules/lint/module_changes.py#L28 Two options: drop Python 3.7 support...
### Description of feature Many tests will pull form the github repo. 55 in total. This means running the tests once already pulls 55 times, running them repeatedly every couple...
The `onComplete` email code was written before nextflow had native support. It adds loads of boiler plate code to every pipeline which can be almost entirely removed now. Needs refactoring,...
Close #1736 Don't add the prefix `https://github.com` to the link created by nf-core modules info. Make the link clickable if `self.remote_location` starts by 'http' The command was also failing when...
### Description of feature The pytests for the `nf-core modules` commands are very slow. I believe this partly due to that every test pulls several remote git repositories in the...
### Description of the bug When running `nf-core modules lint` on a module which contains a label not starting `process_` an `AttributeError` is raised and the process errors out. It...
### Description of the bug The link created by `nf-core modules info` is broken since the move from the github api. The link is set on https://github.com/nf-core/tools/blob/dev/nf_core/modules/info.py#L164-L168, but the `self.remote_location`...