These are chat archives for nextflow-io/nextflow

12th
Feb 2019
Alexey Dushen
@blacky0x0
Feb 12 14:07
Is there a story or history about development of NextFlow? Why it was created and what for?
Félix C. Morency
@fmorency
Feb 12 14:10
Because @pditommaso was tired of hadoop. :laughing:
Paolo Di Tommaso
@pditommaso
Feb 12 14:11
there's a story of 5 years development and millions of jobs deployed in production environment in a large number of top research institutes and life science orgs and startups such as Roche, Boehringer Ingelheim, Enterome, Sanger, IARC, SciLifeLab, The Crick Institute, EMBL-EBI, and many others
Alexey Dushen
@blacky0x0
Feb 12 14:11
ahhah, hadoop, lol, counted)
Paolo Di Tommaso
@pditommaso
Feb 12 14:11
Because @pditommaso was tired of hadoop.
this is a good summary :satisfied:
Luca Cozzuto
@lucacozzuto
Feb 12 14:11
@pditommaso yeah but why did you started it?
And in particular, how much beer did you drink before?
Maxime Garcia
@MaxUlysse
Feb 12 14:15
LifeScienceLab ?
That's a new one ;-)
Paolo Di Tommaso
@pditommaso
Feb 12 14:16
oops SciLifeLab ..
Maxime Garcia
@MaxUlysse
Feb 12 14:17
I think the fake name I prefer is SciFiLab
Paolo Di Tommaso
@pditommaso
Feb 12 14:18
The Nat Biotech paper give also some technical insight about the project
Alexey Dushen
@blacky0x0
Feb 12 14:27
It's interesting, thanks
Paolo Di Tommaso
@pditommaso
Feb 12 14:28
@hydriniumh2 upload are verified with a md5 checksum as per AWS API, not sure it's doing the same for downloads
Alexey Dushen
@blacky0x0
Feb 12 14:33

too excited to share this, are you ready for NF script 2.0 ?

btw, it looks like ENUMS in JAVA with the arguments. a little bit weird, but i need to get used to it. Are you trying to get rid of AST transformations?

Paolo Di Tommaso
@pditommaso
Feb 12 14:34
it looks like ENUMS in JAVA with the arguments
what do you mean ?
ahhh, the capitalisation
Alexey Dushen
@blacky0x0
Feb 12 14:34
yep
Paolo Di Tommaso
@pditommaso
Feb 12 14:35
that's just a stylistic attempt, it's not supposed to be enforced
hydriniumh2
@hydriniumh2
Feb 12 14:35
@pditommaso Ah, ok thats what I was afraid of
Paolo Di Tommaso
@pditommaso
Feb 12 14:37
the main point chance is that the syntax improvement allows the invocation of workflow tasks a plain function and to reference outputs as an attribute of the task itself
Mathias Walzer
@mwalzer
Feb 12 16:45
Hi there
I have some issue with the execution of nextflow workflows in a slurm cluster with singularity container jobs
would you know any immediate workaround?
Félix C. Morency
@fmorency
Feb 12 16:51
@mwalzer add the bind path to your singularity.conf.
Mathias Walzer
@mwalzer
Feb 12 16:56
I'll try that just now
Would this work if I add this in my *.nf nextflow.config?
and where would I have to put it
Mathias Walzer
@mwalzer
Feb 12 17:02
well, adding it in the workflow works
would be nice though, if the workflow description would be agnostic of the execution system (and hence filesystem pecularities) - like nextflow already has with the --profile option
Alexander Peltzer
@apeltzer
Feb 12 17:46
You can add that to your confit profile or ask an admin to edit the singularity config
Thats what we did everywhere - it’s typically just a one time thing and then done
Phil Ewels
@ewels
Feb 12 22:14
Yes, note that nextflow can have multiple config files in multiple locations. Notably one in a user’s home directory. If placed there then the workflow stays agnostic and it will also make all nextflow workflows work...