These are chat archives for nextflow-io/nextflow

22nd
Feb 2017
Tiffany Delhomme
@tdelhomme
Feb 22 2017 09:18 UTC

Hi all, I have a variable defined in my config file

mem_default = '4'

and I would like to custom it when launching my pipeline, does anyone have an idea for that?

Paolo Di Tommaso
@pditommaso
Feb 22 2017 09:35 UTC
define it as a params or an env variable
Tiffany Delhomme
@tdelhomme
Feb 22 2017 09:43 UTC
Thanks! I defined it as an env variable but do not know how to custom it when running my pipeline, --mem_default 8 does not work
Paolo Di Tommaso
@pditommaso
Feb 22 2017 10:16 UTC
umm
as param it should be defined as
params.mem_default = '4'
then should should be able to override as --mem_default 8
Tiffany Delhomme
@tdelhomme
Feb 22 2017 10:21 UTC
if I define it in the params scope I get
Not a valid 'memory' value in process definition: [:].GB
Paolo Di Tommaso
@pditommaso
Feb 22 2017 10:22 UTC
it looks more you put it in the process not params
Tiffany Delhomme
@tdelhomme
Feb 22 2017 10:24 UTC

actually in params I have

mem_default = '4'

and in process I have

memory = { task.exitStatus == 130 ? "${mem_default}.GB" * task.attempt : "${mem_default}.GB" }
and this works if mem_default is defined in env scope...
Paolo Di Tommaso
@pditommaso
Feb 22 2017 10:26 UTC
then you need to reference it as params.mem_default in the config
because it's not a config var anymore but a params
Tiffany Delhomme
@tdelhomme
Feb 22 2017 10:27 UTC
ok I see! I will try
Tiffany Delhomme
@tdelhomme
Feb 22 2017 10:45 UTC
hum... actually it is not a parameter of the pipeline, as an example I want to run helloworld first time with mem_default as 4 and second time at 8, but my idea was to do not change config file between two runs and so specify my memory at the time I launch the pipeline
Tim Diels
@timdiels
Feb 22 2017 19:36 UTC
What does NextFlow offer to answer "What is the pipeline doing right now? What has failed?". Ideally this would be presented visually instead of as a long list of traces, does this already exist?
Paolo Di Tommaso
@pditommaso
Feb 22 2017 20:00 UTC
Currently NF is a command line tool and does not provide an interactive GUI for information.
It must also be said that it most common scenario it is used to submit jobs to a batch scheduler such SLURM or SGE, thus you may rely on the accounting of that system to track the jobs under executions
however regarding errors NF is quite explicit, it stop reporting the error cause and the directory on which the failed task was executed.
Tim Diels
@timdiels
Feb 22 2017 20:10 UTC
Alright, though I will say, NextFlow is really impressive.
Paolo Di Tommaso
@pditommaso
Feb 22 2017 20:10 UTC
I'm happy you are enjoying it
Tim Diels
@timdiels
Feb 22 2017 20:11 UTC
Does -resume take into account changes in input files? Rerunning the job/process if so.
Paolo Di Tommaso
@pditommaso
Feb 22 2017 20:11 UTC
yes of course