Skip to content

Shared code for the R scripts #101

Open

Description

@MaximilianStammnitz

Suggested by @maxulysse in #54. Several module templates copy the same R code instead of sharing it, e.g.:

  • the false-doubles estimators seq_error_correct_by_false_doubles_MLE and seq_error_correct_by_false_doubles_EB share most of their code
  • correct_library_completed and seq_error_correct_counts_for_heatmaps are defined in both error-correction templates (false doubles and wildtype);
  • position_biases is defined in both global_pos_biases templates.

To decide together with nf-core team: shared code either in bin/ (a small R file sourced by the templates, or whole scripts), or templates that stay self-contained. The current nf-core module specification recommends templates as the most portable option, while bin/ would avoid copies.

Best done together with the planned v1.1.0 performance overhaul. In this, we will likely merge several of the current processes to reduce unnecessary scheduling.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Labels

enhancementNew feature or request

Type

No type

Projects

No projects

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions