These are chat archives for nextflow-io/nextflow

1st
Feb 2019
micans
@micans
Feb 01 11:26
@lastwon1216 there is something wrong with your script section. This shell command you show contains nextflow code, for example --readFilesIn ${reads}. As I said earlier, your prefix variable does not make sense; it seems to me you are trying to do too much at the same time, or you are making changes to an existing pipeline whilst not fully understanding the code in that pipeline. Are you doing the latter (changing an existing pipeline) or the former (making a new pipeline yourself)?
lastwon1216
@lastwon1216
Feb 01 19:13
@micans I think I am in the middle, since I already have a bash script for rnaseq, but trying to translate them into nextflow based upon https://www.nextflow.io/example4.html
slowsmile
@slowsmile
Feb 01 19:56
Hi, I wonder what rules does nextflow have on logic operators? Does it recognize True, true, T, or False. DIdn't see that in manual
in my practice I want to use a flag e.g. --flag to indicate whether I want to run a certain process or not
but do I have to give it a value like --flag True?
or I can simply put the option there to indicate my choice? like --flag
Paolo Di Tommaso
@pditommaso
Feb 01 20:01
boolean values are true and false
--flag w/o value is implicitly true
slowsmile
@slowsmile
Feb 01 20:04
thanks for the clarification!
lastwon1216
@lastwon1216
Feb 01 21:53
in bash shell, command line of ./loadGenome.sh Mouse Test would work, but not through nextflow :(