ejh243 / BrainFANS

Complex Disease Epigenomics Group's quality control and analysis pipelines for DNA methylation arrays, SNP arrays, BS-Seq, ATAC-Seq and ChIP-Seq

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137 bug add scripts directory variable to config #139

Closed ejh243 closed 5 months ago

ejh243 commented 6 months ago

Description

This pull request will simplify use of config files with DNAm pre-processing pipeline and remove need to use relative paths when executing scripts.

Issue ticket number

This pull request is to address issue: #137 .

Also closes #117, #52, #145

Type of pull request

[X] Bug fix
[ ] New feature/enhancement
[X] Code refactor
[X] Documentation update

Checklist

[X] I have performed a self-review of my own code
[ ] I have commented my code, particularly in hard-to-understand areas
[X] I have tested my code to check that it is functional
[ ] I have used linters to check for common sources of errors
[ ] I have implemented fail safes in my code to account for edge cases
[X] I have made the corresponding changes to the documentation

ejh243 commented 6 months ago

@AnthonyKl98 @alicemfr I have changed the location of the log/error files in the job submission script so it should no longer fail as a results of this. Could you retest?

ejh243 commented 6 months ago

@rhaigh5 can you update your versions of the scripts and test? I added the installLibraries script to the job submission script.

sof202 commented 5 months ago

Just to let you know @alicemfr, when you are saving array/DNAm/preprocessing/installLibraries.r, you are saving it with carriage return sequences (CRLF end of line). Make sure your text editor is using LF as otherwise the files you are changing might break. I don't think it is a problem for R scripts, but it will be if your text editor does the same with any bash scripts. It also makes it very hard to look at commit differences.

(^M is a literal carriage return, #43)

sof202 commented 5 months ago

The same goes for: array/DNAm/preprocessing/checkColnamesFunction.r array/DNAm/preprocessing/README.md (though this isn't being executed so it doesn't matter) array/DNAm/preprocessing/checkColnamesSampleSheet.r array/DNAm/preprocessing/normalisation.r

ejh243 commented 5 months ago

I have tested and am happy so am going to merge.