These are chat archives for nextflow-io/nextflow

27th
Feb 2017
Paolo Di Tommaso
@pditommaso
Feb 27 2017 08:15
@karinlag :clap: :clap:
Félix C. Morency
@fmorency
Feb 27 2017 22:02
is there a way to perform a dry-run and output which input file changed (if any)?
Paolo Di Tommaso
@pditommaso
Feb 27 2017 22:03
oh, do you mean to infer what input changed ?
Félix C. Morency
@fmorency
Feb 27 2017 22:04
yes
Paolo Di Tommaso
@pditommaso
Feb 27 2017 22:04
nope :/
Félix C. Morency
@fmorency
Feb 27 2017 22:04
I think NF does it internally
but it would be nice to be able to output the result somewhere
Paolo Di Tommaso
@pditommaso
Feb 27 2017 22:04
internally it does, but there isn't such dry-run concept in NF
amacbride
@amacbride
Feb 27 2017 23:12
@pditommaso In the task accounting (pipeline_trace), is there any way to get the node on which the task executed? (For example, with SLURM, the execution environment for the script has SLURMD_NODENAME set -- I was wondering if there might be a way to get that back to NF for output in the trace file.)
Paolo Di Tommaso
@pditommaso
Feb 27 2017 23:13
unfortunately not, though it should be reported in the .nextflow.log
we should improve it at some point
amacbride
@amacbride
Feb 27 2017 23:15
I see an indication that it's been submitted, but not on which node it's been run. OK, I will figure out another way to track it, thanks!
Paolo Di Tommaso
@pditommaso
Feb 27 2017 23:15
let me check
it not reported by default
you can enable with
nextflow -trace nextflow.scheduler.Scheduler run .. etc
amacbride
@amacbride
Feb 27 2017 23:19
Ah, got it -- so it's set on a class-by-class basis?
Paolo Di Tommaso
@pditommaso
Feb 27 2017 23:20
what?
the logging you mean ?
amacbride
@amacbride
Feb 27 2017 23:23
Yes -- it wasn't clear from the docs what NXF_TRACE does, vs. trace config in the config file, vs. -trace vs. -with-trace, etc.
Paolo Di Tommaso
@pditommaso
Feb 27 2017 23:25
NXF_TRACE is the same of -trace and enable NF internal logging
trace config and -with-trace enable pipeline process executions tracing/profiling
amacbride
@amacbride
Feb 27 2017 23:27
got it -- so -trace won't override anything I set in the trace context in the config file?
Paolo Di Tommaso
@pditommaso
Feb 27 2017 23:27
exactly, it's a complete different thing
-trace takes comma separated list of class or package names
amacbride
@amacbride
Feb 27 2017 23:28
Thank you for clarifying, I never would have figured that out.
Paolo Di Tommaso
@pditommaso
Feb 27 2017 23:28
there are so many things ...
this channel is here for that
amacbride
@amacbride
Feb 27 2017 23:28
:)