Added separate param for setting qval threshold for pathway analysis

[WackerO]

... in order to allow different values for the qval in DE analysis and pathway analysis. If not set by the user, the pathway analysis will continue to use the same threshold as for DE analysis.

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[tillenglert]

LGTM! One question though, is the threshold working on adjusted pvalues, or raw values? It's a bit misleading that the adjusted pval threshold is used if this one is not set, but I couldn't find anything about the pathway_pval_threshold being used on adjusted pvals! So all in all if the new param works on adjusted pvals, you could append that to the help text in the nextflow_schema.json and Execute_report.R

[WackerO]

Many thanks, Till! Yes, it's adjusted, good point. I'll change the param name and descriptions :)