A changed tophat/runnow.tmp has no influence on the downstream stages (i.e. cufflinks, htseqcount, bamann).
currently all runnow.tmps need to be edited when RUNTOPHATCUFFHTSEQ is run in keep+armed mode
A better way would be to somehow propagate that the shot-list though
A changed tophat/runnow.tmp has no influence on the downstream stages (i.e. cufflinks, htseqcount, bamann).
currently all runnow.tmps need to be edited when RUNTOPHATCUFFHTSEQ is run in keep+armed mode
A better way would be to somehow propagate that the shot-list though