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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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The CLI option --scheme-directory does nothing #46

Closed sylvinite closed 2 years ago

sylvinite commented 2 years ago

What needs to be done: The CLI option --scheme-directory needs to overwrite what is posted in the config

Suggestions on how to get it done: Review the currently working options. Copy paste.

What are the arguments for getting it done: Intuitively CLI options take precedence over config options

Task is considered finished when: The CLI option --scheme-directory does what is intuitively expected

JD2112 commented 2 years ago

Issues #46

WHAT has done

  1. Changed the base.config file; now primer sets will be downloaded from the genomic-medicine-sweden repo instead artic-network/primer-schemes
  2. Default primer set is - midnight V1
  3. Primer set for each protocol added separately to the repo. Artic nanopolish cannot handle '/' in the repo name.

HOW to use CLI-option

  1. --scheme-directory artic-primer/V3/.
  2. README updated - how to use --scheme-directory.
JD2112 commented 2 years ago

Updates issue #46

  1. --scheme required to run the pipeline.
  2. --scheme will add the primers from the repo list.
  3. Details of use can be found on README.