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Add lipidomics workflow to MetaMS (cli, wdl) #32

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7 of 8 tasks
kheal opened this issue Mar 26, 2024 · 1 comment
Open
7 of 8 tasks

Add lipidomics workflow to MetaMS (cli, wdl) #32

kheal opened this issue Mar 26, 2024 · 1 comment
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@kheal
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kheal commented Mar 26, 2024

This cannot be finished until CoreMS 3.0 is released

Drafting subtasks

  • Write metaMS.lcmsLipidomicsWorkflow module
  • Update metaMS.cli module to source metaMS.lcmsLipidomicsWorkflow module
  • Add second wdl for second workflow for lcmsLipidomicsWorkflow
  • Change name of metams_input.json to specify that it is specific to the GCMS-metabolomics workflow
  • Add .json that is specific to the parameters for the LCMS-lipidomics workflow (similar to the exisiting metams_input.json file)
  • Add lipidomics workflow information to MetaMS Readme
  • Update docker image
  • Update requirements to CoreMS 3.0
@kheal
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kheal commented Oct 3, 2024

This is drafted in lipid_dev branch of MetaMS, blocked by the release of CoreMS 3.0

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