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[Documentation Fault]: Repeated and incomplete information in README #252

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sof202 opened this issue Nov 13, 2024 · 0 comments
Open

[Documentation Fault]: Repeated and incomplete information in README #252

sof202 opened this issue Nov 13, 2024 · 0 comments
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documentation Faults in the documentation

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@sof202
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sof202 commented Nov 13, 2024

Fault type

Incorrect/outdated information given

Please describe the fault in detail

In array/DNAm/preprocessing/README.md the following lines are given:

`sbatch 1_runDNAmQC.sh /path/to/configFile`
/path/to/configFile the path to config file which specifics the data and script paths for processing
* executes loadDataGDS.r ${DATADIR}
* executes calcQCMetrics.r ${DATADIR} ${REFDIR} [${GENOFILE}]
* executes clusterCellTypes.r ${DATADIR} ${RCONFIG}
* executes Rscript -e "rmarkdown::render('QC.rmd', output_file='QC.html')" --args ${DATADIR} ${RCONFIG} $USER

This slurm script however does more than this, making this bulleted list outdated. I would suggest to remove it entirely as it isn't really adding anything to the readme file. If the user wanted to know what R scripts this slurm script ran, they could just look at the files themselves. If they wanted to know the exact commands being ran, they could again just look at the slurm script itself.

Further problem

Also there is some formatting problems that comes with what is currently shown as it is not put inside of backticks:

image

@sof202 sof202 added the documentation Faults in the documentation label Nov 13, 2024
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