stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Check for MACS2 before splitting file #1678

Open AmelZulji opened 3 months ago

AmelZulji commented 3 months ago

When calling peaks using:

peaks <- CallPeaks(
  object = seu,
  group.by = "cell_type",
  macs2.path = "wrong_path"
)

splitting fragments will start before checking whether specified macs2.path points to existing instance of MACS2. It would be nice to first check for MACS2.

timoast commented 3 months ago

What version are you using? This should indeed be happening before splitting files: https://github.com/stuart-lab/signac/blob/8b98f63f89fb988fcfd5e1be6af6de316353008c/R/peaks.R#L80-L89

timoast commented 3 months ago

Ah, nevermind, I see what you're saying. We only check if there is a path, not that there's a functional MACS at that path. Ok, we can try to add that check.

AmelZulji commented 3 months ago

Thank you!