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Feature/icres based grns #22

Merged
merged 16 commits into from
May 23, 2024
Merged

Feature/icres based grns #22

merged 16 commits into from
May 23, 2024

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nicomaper
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This pull request contains the following:

  • Update of the .gitignore file to include the correct matching for the output and error SLURM files.
  • Changes to give the ACR files as a channel to the genome-wide and locus-based workflows, instead of as a string/value parameter. This will make it easier to implement the changes mentioned below to include the "iCREs-based MINI-AC" feature.
  • Necessary script to run this "iCREs-based MINI-AC", including a process that executes a Python script to use the files with the iCREs annotated to their closest gene, to retrieve the coordinates associated with the genes of interest (input).
  • The input gene sets of the example to run the test of this new feature.
  • The corresponding example config file (and a small update on the previous one for the commented annotations, but no change to code)
  • The corresponding documentation update to this new feature.
  • Final update on the .gitignore file to avoid committing confidential files or files that are too large (iCREs BED files).

@nicomaper nicomaper requested a review from hdbeukel May 15, 2024 09:42
@hdbeukel hdbeukel changed the base branch from main to dev May 15, 2024 13:37
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@hdbeukel hdbeukel left a comment

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Nicely done! Some minor comments only.

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@nicomaper nicomaper merged commit 3736ff6 into dev May 23, 2024
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3 participants