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🚀 DSL2 / modules documentation 🚀

16th-18th March 2022

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DSL2/Modules Team


Team Members

  • Harshil Patel
  • Edmund Miller
  • Gregor Sturm
  • Priyanka Surana
  • Jose Espinosa-Carrasco
  • Lasse Folkersen
  • Julia Mir Pedrol
  • Varun Shamanna
  • (Friederike Hanssen)

Tasks

  • Working on "Adding a new pipeline" documentation (PS)
  • Discussion on subworkflows implementation (HP, MG, JE, FH, EM)
  • Fixing meta.yml (Ascat) (LF)
  • Document -stub running (LF)
  • Updating documentation to include stub-running, merged in 1079
  • Add initial intro to meta map (EM, JMP)

Day 2/3

  • Working through modules creation tutorial (VS)
  • Update modules README (VS)
  • Overwriting resource requests, overwriting container definitions, overwriting non-mandatory parameters via task.ext and using params.yml instead of -c to provide parameters, 987 (should be splitted in several issues and it's WIP).

Subworkflow

  • Installing subworkflows with tools:
    • Get a list of modules that need to be installed (how to find them) -> tools needs to install missing modules in pipeline/repo -> install subworkflow (tools command needed, probably once the new people join Seqera/QBiC (next few months))
    • Auto-include on module installation
    • Standard import path (relative path doesn’t match at the moment)
    • Directory structure
    • Md5sums
    • subworkflow.json
  • Testing subworkflows:
    • On module change, subworkflows needs to be tested

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