These are chat archives for nextflow-io/nextflow

25th
Oct 2017
Edgar
@edgano
Oct 25 2017 10:12
I´m using templates in my NF pipeline, and I call a cpp program inside the template (.sh). I am trying to send an integer from the cpp to the sh. I tryed with the return statment and the $? but it doesnt work. any idea how to ?
Paolo Di Tommaso
@pditommaso
Oct 25 2017 10:14
the simplest way should be that you cpp application print that value on the stdout
Evan Floden
@evanfloden
Oct 25 2017 10:14
See here nextflow-io/nextflow#69
Paolo Di Tommaso
@pditommaso
Oct 25 2017 10:15
then in the NF pipeline you capture that with output: stdout into some_channel
Edgar
@edgano
Oct 25 2017 10:16
I only need inside the sh template :) thanks guys, I will try it
Paolo Di Tommaso
@pditommaso
Oct 25 2017 10:17
ahhh
if yes $? should work
but I guess you need to escape $
hence \$?
Edgar
@edgano
Oct 25 2017 10:20
yep, looks great now. I forget the escaping (again) :)
Paolo Di Tommaso
@pditommaso
Oct 25 2017 10:31
:+1:
Joel Lafond-Lapalme
@Lafond-LapalmeJ
Oct 25 2017 11:42
Hi everyone, i am new to nextflow. I am just wondering which editors and settings you are using to have a nicely format nexflow code like in the website examples ? Thank you
Paolo Di Tommaso
@pditommaso
Oct 25 2017 11:48
do you mean here ?
you can use any syntax highlighter setting the groovy programming syntax
Nextflow is a superset of Groovy, therefore is not 100% precise, but it's a good approximation
Joel Lafond-Lapalme
@Lafond-LapalmeJ
Oct 25 2017 12:12
Yes! this is what I was looking for. Thank you
Simone Baffelli
@baffelli
Oct 25 2017 16:05
So, new error for me Oct-25 18:03:01.195 [main] DEBUG nextflow.Session - Session aborted -- Cause: assert !(source instanceof DataflowExpression)
What does is mean? it must be related with buffer somehow
Simone Baffelli
@baffelli
Oct 25 2017 16:11
Ok, maybe I get it
ERROR ~ Operator take cannot be applied to a value channel