These are chat archives for nextflow-io/nextflow

13th
Aug 2018
hydriniumh2
@hydriniumh2
Aug 13 2018 13:38
@ewels Thanks! Definitely sounds like what I'm looking for
Phil Ewels
@ewels
Aug 13 2018 14:16
Cool! It's not super simple but perhaps it could be helpful :) Let's chat in https://gitter.im/nf-core/Lobby for more details :+1:
Guillaume Collet
@gcollet
Aug 13 2018 14:35
HI everyone. I'm trying nextflow for a few days and I am facing a strange behavior. I have a workflow working fine. When I try to launch it with -with-report option, it fails with the following error : .command.stub: line 58: kill: (1758) - No such process
In my process, I use a perl script that opens a file, output some lines on stdout and close the file
Do you have an idea ?
Félix C. Morency
@fmorency
Aug 13 2018 14:40
@gcollet Can you post the code somewhere?
Guillaume Collet
@gcollet
Aug 13 2018 14:44
Félix C. Morency
@fmorency
Aug 13 2018 14:46
@gcollet do you have a SampleSheet.csv I could use?
Guillaume Collet
@gcollet
Aug 13 2018 14:47
ho yes
added to the pad
I tried with an awk script... It works
I suppose it comes from perl
Félix C. Morency
@fmorency
Aug 13 2018 14:52
What's the command-line you're using? I just nextflow run -with-report TEST.html ../main.nf and everything worked just fine
Guillaume Collet
@gcollet
Aug 13 2018 14:54
nextflow run main.nf -with-report
Félix C. Morency
@fmorency
Aug 13 2018 14:54
Runs fine here :(
Guillaume Collet
@gcollet
Aug 13 2018 14:55
I'am on macos
Félix C. Morency
@fmorency
Aug 13 2018 14:55
Mmm maybe that's why. I'm on linux
Maybe you're missing a dependency.
Guillaume Collet
@gcollet
Aug 13 2018 14:56
I have to investigate
or a pb with process managment
Thank you for your help
I will use the awk script instead
Félix C. Morency
@fmorency
Aug 13 2018 14:57
@gcollet See the Note and Warning blocs @ https://www.nextflow.io/docs/latest/tracing.html#tasks
Evan Floden
@evanfloden
Aug 13 2018 16:37
@gcollet I saw this last week running on MacOS as well. I put it down to using '-with-trace' but was not able to determine the exact cause however.
Evan Floden
@evanfloden
Aug 13 2018 16:43
Going back, my error was:
Command error:
  .command.stub: line 58: kill: (12521) - No such process
I put it down to not being able to capture these using -with-report and -with-trace on MacOS.
David Mas-Ponte
@davidmasp
Aug 13 2018 16:54
hi, I have a question regarding the conda integration. I checked in the .command.run script how nextflow activates the environtment (by local path in my case). I saw it's doing a source activate /path/to/env right? We saw that since conda 4.4 they are suggesting to use conda activate instead (see SO and release notes).
Is there any reason why nextflow is using source activate?