Since my DNA methylation data were generated from the whole blood, I set cellcounts_required="yes" and measured_cellcounts="NULL" in my config file. This configuration causes the 03a script to skip the step of "Comparing measured with predicted cell counts," and as a result, no /results/03/cor_plot.pdf is generated.
However, the ./check_upload.sh script currently checks for the existence of /results/03/cor_plot.pdf regardless of the dataset's specific configuration. Consequently, the absence of this file leads to a failure when running ./check_upload.sh.
To address this issue, I suggest enhancing the ./check_upload.sh script by adding conditional checks for output files based on the specific configuration of the dataset.
Contact Details
s.w.wang@exeter.ac.uk
Path to affected file
Type of refactor
Edge case error handling
Description of required code refactor
Since my DNA methylation data were generated from the whole blood, I set
cellcounts_required="yes" and measured_cellcounts="NULL"in my config file. This configuration causes the 03a script to skip the step of "Comparing measured with predicted cell counts," and as a result, no/results/03/cor_plot.pdfis generated.However, the
./check_upload.shscript currently checks for the existence of/results/03/cor_plot.pdfregardless of the dataset's specific configuration. Consequently, the absence of this file leads to a failure when running./check_upload.sh.To address this issue, I suggest enhancing the
./check_upload.shscript by adding conditional checks for output files based on the specific configuration of the dataset.Thank you.