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sanger-tol / readmapping

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
https://pipelines.tol.sanger.ac.uk/readmapping
MIT License
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Re-enable remote reference lookup for CRAM #137

Open tkchafin opened 1 month ago

tkchafin commented 1 month ago

Description of feature

Work in ref_cache which branches dev, but some changed might also need to go into patch (=1.3.2).

  1. Re-enable remote reference lookup as fall-back for SAMtools. This was encountered as an issue in a case that pipeline inputs were pre-aligned.
  2. Whitelist REF_PATH and REF_CACHE for all execution back-ends
  3. Do we need to stage REF_CACHE (e.g., https://github.com/epi2me-labs/wf-basecalling)??