These are chat archives for nextflow-io/nextflow

25th
Jan 2019
Jason Yamada-Hanff
@yamad
Jan 25 00:10
iiuc, channel_name.collect() will do what you want
Rad Suchecki
@rsuchecki
Jan 25 00:15
@yamad there is, for example if you declare your input as a value then you can create the symlinks yourself, but not sure if that's worth the extra effort
e.g. val(arr) from out_ch_one.toList() to get a list of [name, file] tuples
@Puumanamana its not clear to me if you mean many instances of the same process or just the one
Cedric
@Puumanamana
Jan 25 00:26
@rsuchecki I'm not sure what you mean either :). My processes have many inputs coming from a given channel. Once the channel is empty, I want to run a script to summarize the content of the process' outputs. And I want to do that for each process I have.
Rad Suchecki
@rsuchecki
Jan 25 00:32
:-)
ok, so many inputs as separate emissions from a channel so the process is executed once per each emission and you want a summary for all runs of that process
Rad Suchecki
@rsuchecki
Jan 25 00:39
in which case .collect() is a good start, as indicated above
rfenouil
@rfenouil
Jan 25 08:20
@MaxUlysse Thanks for the invite, I'll actually think about it but I'll let you know in advance ;)
Vassily Trubetskoy
@vtrubets
Jan 25 13:35
quick question: what is the google cloud cluster support built on? Is this using the elasticluster or something purpose built?
I've started looking through the codebase, but cannot yet find where this is defined
Paolo Di Tommaso
@pditommaso
Jan 25 14:30
no, it's managed by NF itself
Vassily Trubetskoy
@vtrubets
Jan 25 14:31
Good to know -- thank you!
Paolo Di Tommaso
@pditommaso
Jan 25 14:31
welcome
Tyler Biggs
@biggstd
Jan 25 17:36
I have a process with multiple optional output files. It is part of a recursive workflow. I am having trouble finding an elegant way to have the workflow terminate if this process does not produce any output. Any advice?
I basically need to check if a process produced any files before it exited, and if not, gracefully exit the workflow.
Caspar
@caspargross
Jan 25 17:46
is there a way to access workflow properties of a running nextflow instance? I would like to create an external tool that is monitoring nextflow process and parameters.
Félix C. Morency
@fmorency
Jan 25 18:54
is there a way to spot unused channel variables?
Jason Yamada-Hanff
@yamad
Jan 25 19:10
@biggstd .isEmpty()won't do it?
najitaleb
@najitaleb
Jan 25 19:57
I just configured udocker and I already have docker on my machine. I'm getting this error when I try to run a nextflow file and I'm not sure how to disable the container engine i want. ERROR ~ Cannot enable more than one container engine -- Choose either one of: docker, udocker . Is there a way to fix this issue?
Tyler Biggs
@biggstd
Jan 25 19:59
@yamad I'm trying variations of that now, while that seems to work for detecting if a process returns an empty list, the workflow still doesn't seem to want to terminate. I suspect this is because of the circular layout of my processes. I may try to create a MWE to share if things keep going poorly, thanks.