Change outdir subdirectory names to module names

nf-core / mcmicro

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

https://nf-co.re/mcmicro

MIT License

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Change outdir subdirectory names to module names #19

Closed jmuhlich closed 3 months ago

jmuhlich commented 3 months ago

Description of the bug

Subdirectories should be named after the corresponding module name, with possible parallel outputs from different tools under different names or sub-sub-directories therein. E.g. instead of ashlar/ we should have registration/.

Command used and terminal output

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Relevant files

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System information

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RobJY commented 3 months ago

I've pushed a fix that moves ashlar output to $outdir/registration/ashlar

I'm thinking for the other modules we would have superdirectories named:

input_validation for input_check.nf
illumination_correction for basicpy
segmentation for deepcell_mesmer
quantification for mcquant

Please let me know if I should change any of the above.

RobJY commented 3 months ago

just pushed updated code to fix this as described above