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EBI-Metagenomics / genomes-catalogue-pipeline

MGnify genome analysis pipeline
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Migration to nextflow [WIP] #34

Closed mberacochea closed 1 year ago

mberacochea commented 1 year ago

Migration from the bash script approach to nextflow.

I've migrated the scripts too, ran black to format them and did some minor refactoring to improve / adjust features.

I need to adjust some of the unit tests and link Jenkins as the CI/CD

KateSakharova commented 1 year ago

Huge amazing work, Martin! Thank you :) The only thing I care about is containers for some tools (I added comments with examples). Some modules use only tools that we can replace with biocontainers of needed version. And add python/perl/biopython containers for custom scripts.

mberacochea commented 1 year ago

The review process was done outside github.