Open SiyiSEA opened 4 days ago
If we did force the cellcounts_required = "yes",
Would that be more safe for us to delete the parameter of cellcounts_required
in the config file?
And update the wiki description about the cell count? https://github.com/genetics-of-dna-methylation-consortium/godmc_phase2/wiki/Install-and-set-up#cell-count-data
I could do them before the merging.
Currently it seems like recalculation of cell counts is not enforced, i.e. if cellcounts_required
is set to no, this will be skipped. Should this be the case @epzjlm ?
Looking at the wiki I wonder if this is because sorted datasets don't need cell composition caluclated? But is this is the case can't we use the sorted_methylation
config variable to turn this off? Otherwise we might get whole blood datasets not running this.
It might be easer to add a check to script 01 or script 03
This pull request is for:
check_upload.sh 03a check
to handle the situation whencellcounts_required="yes" and measured_cellcounts="NULL"
have been set in the config file;