These are chat archives for nextflow-io/nextflow

29th
Mar 2019
Carl Witt
@carlwitt
Mar 29 09:03
I forgot to specify -with-timeline. Can I still generate a timeline report, maybe from .nextflow.log?
Phil Ewels
@ewels
Mar 29 09:52
Don't think so sorry
I think you can probably re-run with -resume which will use cached tasks for everything, which may give you a semi-useful timeline report.
I think it uses the previous stats in places, though it may just say 1s for everything
Question - I vaguely remember a nextflow feature where tasks can be grouped so that, for example, each sbatch job submission has 10 smaller tasks within it.
Did I dream this? If not, what's the name / where can I find documentation?
Paolo Di Tommaso
@pditommaso
Mar 29 10:02
yes, i've made some experimental implementation on task grouping (can't find the GH issue now)
but it turned out to be more challenging then expected
Chelsea Sawyer
@csawye01
Mar 29 10:38
@tobsecret @micans Thanks for your help!
KochTobi
@KochTobi
Mar 29 13:50
@sivkovic do you mean the EBS scaling from https://github.com/aws-samples/aws-genomics-workflows ?
Sinisa Ivkovic
@sivkovic
Mar 29 14:32
@KochTobi yes that one.
Félix C. Morency
@fmorency
Mar 29 14:33
which NF variable controls the location of the work directory? Can we change it directly in the main.nf?
micans
@micans
Mar 29 15:59
@fmorency Is the -w command line parameter not sufficient?
Phil Ewels
@ewels
Mar 29 16:22
@pditommaso - ok thanks, so I'm not going crazy :laughing:
Paolo Di Tommaso
@pditommaso
Mar 29 16:23
no .. i'm going crazy ;)
Félix C. Morency
@fmorency
Mar 29 16:56
@micans ah yes! I think I need more coffee