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Prototype for batch submission

Klitos Savva requested to merge PR-Prototype_BatchSubmission into master

Prototype version for batch submission Notes:

  • Jobs for each single file
  • Need to make sure that names of files in the output folder have a sensible format to be able to check and re-run the jobs if they have failed (Todo)
  • Need to have a different version for conda environment users. This is set up for micromamba for now.

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