These are chat archives for nextflow-io/nextflow

20th
Oct 2016
Félix C. Morency
@fmorency
Oct 20 2016 13:52
morning
Mokok
@Mokok
Oct 20 2016 14:04
a canadian morning* here in europe it's 4pm :D
Félix C. Morency
@fmorency
Oct 20 2016 14:04
:D
Mokok
@Mokok
Oct 20 2016 14:05
is Paolo still locked in his room ?
(just curious, no question today :p )
Evan Floden
@evanfloden
Oct 20 2016 14:06
We let him out today, but only to go to a workshop.
He is on strict instruction to return to Gitter when it is over, should only be a couple more hours I guess
Mokok
@Mokok
Oct 20 2016 14:11
Poor Paolo :D
Félix C. Morency
@fmorency
Oct 20 2016 14:36
if(params.help) {
    usage = file("$baseDir/USAGE")
    print usage.text
    return
}
is there a way to refer to some variable in USAGE and print the value of those when using --help?
Evan Floden
@evanfloden
Oct 20 2016 15:35
Is it posible for downstream tasks to begin, prior to the completion of the publishDir command?
Paolo Di Tommaso
@pditommaso
Oct 20 2016 17:20
@skptic regarding this
Is it posible for downstream tasks to begin, prior to the completion of the publishDir command?
what do you mean exactly ?
This message was deleted
@fmorency about this
is there a way to refer to some variable in USAGE and print the value of those when using --help?
Paolo Di Tommaso
@pditommaso
Oct 20 2016 17:26
not out of the box
but you can implement that with a SimpleTemplateEngine
Félix C. Morency
@fmorency
Oct 20 2016 17:36
oh cool
fmorency @fmorency knows nothing about groovy
Paolo Di Tommaso
@pditommaso
Oct 20 2016 17:43
it's an easy lang
Félix C. Morency
@fmorency
Oct 20 2016 17:44
yeah so far so good
Mike Smoot
@mes5k
Oct 20 2016 17:48
There's also this feature request for usage: nextflow-io/nextflow#144, although I've done nothing about it...
Félix C. Morency
@fmorency
Oct 20 2016 17:50
yeah this is related
Félix C. Morency
@fmorency
Oct 20 2016 17:56
SimpleTemplateEngine works
a bit cumbersome, but it works
Paolo Di Tommaso
@pditommaso
Oct 20 2016 19:29
@amacbride Your solution looks fine. Are the alignment process outputs used by different processes or by the same ?