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TODO.md

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The roadmap ahead:

  1. merging Eric's branches and the ATAC_seq branch
  2. making sure sea-snap runs smoothly with newer versions of snakemake (it doesn't currently) --> DONE for mapping pipeline if snakemake version = 7.19.1
  3. making the step from drmaa to cluster profiles --> mostly DONE for mapping pipeline
  4. optimizing resource requirements in mapping_pipeline.snake (check mem vs mem_per_cpu) and adding them to DE_pipeline.snake
  5. allowing sample-specific indices for bwa / salmon / kallisto?
  6. adapting the conda_env.yaml files