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Use ffq to fetch id metadata

Open drpatelh opened this issue 3 years ago • 0 comments

Description of feature

We should try to strip out the custom Python scripts I initially wrote for this pipeline. They have worked relatively well but are fragile to breakages in the standard database APIs. This would be true for any tool querying those databases, however, it would be nice to should replace the custom scripts with a more conventional tool. ffq seems to be the perfect tool for this and I have created an nf-core/module and installed it in the pipeline in https://github.com/nf-core/fetchngs/pull/100 We now need to mould this into a fully fledged implementation.

drpatelh avatar Jul 21 '22 08:07 drpatelh