initial working version of refgenie integration

[KevinMenden]

Adding support for automatic updating of nextflow config files with a refgenie database.

If a refgenie database is used and updated, the update_config() function is triggered, which:

• gets the refgenie configuration file
• looks for the path to the refgenie_genomes.config file in the refgenie config file or in NXF_REFGENIE environment variable
• if both are not given, defaults to $NXF_HOME/nf-core/refgenie_genomes.config
• overwrites the refgenie_genomes.config with the latest refgenie database
• adds an includeConfig statement to the $NXF_HOME/config file if not already existing

This is still very much a WIP, especially with respect to robustness/bugs.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #1090 (8e04b61) into dev (ee54b9f) will increase coverage by 0.22%.
The diff coverage is 76.00%.

@@            Coverage Diff             @@
##              dev    #1090      +/-   ##
==========================================
+ Coverage   64.68%   64.91%   +0.22%     
==========================================
  Files          55       56       +1     
  Lines        6338     6428      +90     
==========================================
+ Hits         4100     4173      +73     
- Misses       2238     2255      +17     

Impacted Files	Coverage Δ
nf_core/refgenie.py	76.00% <76.00%> (ø)
nf_core/modules/modules_command.py	87.80% <0.00%> (+4.87%)	⬆️
nf_core/modules/module_test.py	54.79% <0.00%> (+6.51%)	⬆️

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[nsheff]

Hey, this is great! One suggestion is to add a note into the NF_CFG_TEMPLATE, something like:

NF_CFG_TEMPLATE = """
# This is a read-only config file managed by refgenie. Manual changes to this file will be overwritten
# To make changes here, use refgenie to update the reference genome data
params {{
  genomes {{
{content}
  }}
}}
"""

[KevinMenden]

Good idea thanks!

[ewels]

TODO:

• Fix merge conficts
• Get CI to pass
• Test functionality
• Merge ✅

[mirpedrol]

Tested with:

1. Initialize refgenie: refgenie init -c refgenie-config.yml
   refgenie_genomes.config is created at ~/.nextflow/nf-core/refgenie_genomes.config
   an includeConfig statement is added at ~/.nextflow/config
2. Download a new asset: refgenie pull t7/fasta -c refgenie-config.yml
   refgenie_genomes.config file is updated with the genome path

[ewels]

an includeConfig statement is added at ~/.nextflow/nf-core/config

I think this should be ~/.nextflow/config, no?

cf. https://www.nextflow.io/docs/latest/config.html#configuration-file

The config file $HOME/.nextflow/config

[mirpedrol]

I think this should be ~/.nextflow/config, no?

It is! It was a typo in my comment. I edit the comment to avoid confusion, thanks for spotting it!

[ewels]

It is! It was a typo in my comment.

Yes I was looking for the error in the code and couldn't see it, so was beginning to wonder! 😅

[ewels]

Follow-on PR needed to document usage here: https://nf-co.re/docs/usage/reference_genomes

[ewels]

Can't believe it's finally merged! 👏🏻 🚀 🤩

Awesome work @KevinMenden @mirpedrol 😀