Now, SnpEff will simply exit if called with the multi-threading option -t. This is true also for the current latest SnpEff release at the time of writing, 5.0e.
However, the main SnpEff branch on GitHub seems to have enabled multi-threading again. So, I propose that CovGen use SnpEff multi-threading only if the user asks for it explicitly via CovGen command-line option.
The bash script calls SnpEff with the multi-threading
-t,https://github.com/tgen/CovGen/blob/fc0fff88b21d5bc2fb5e549da012055231b6a67a/CovGen#L468-L469
But this options has been disabled in SnpEff since this commit: https://github.com/pcingola/SnpEff/commit/8c83c049#diff-b4677aba81de865cb08bdc99d3ba9d341955403b69e491fd2b0f9020c44d4187L1101-R1204
Now, SnpEff will simply exit if called with the multi-threading option
-t. This is true also for the current latest SnpEff release at the time of writing, 5.0e.However, the main SnpEff branch on GitHub seems to have enabled multi-threading again. So, I propose that CovGen use SnpEff multi-threading only if the user asks for it explicitly via CovGen command-line option.