These are chat archives for nextflow-io/nextflow

6th
Mar 2017
Daniel E Cook
@danielecook
Mar 06 2017 03:03
Is there a way to re-run a specific process and is it possible to transfer files from a cached process?
Paolo Di Tommaso
@pditommaso
Mar 06 2017 10:51
@danielecook there is no such feature, but if you need to re-execute just a single task you can change to the task work dir and execute it with bash .command.run or qsub .command.run if you are using a batch scheduler
Paolo Di Tommaso
@pditommaso
Mar 06 2017 13:47
A new snapshot including two new operators is available
Félix C. Morency
@fmorency
Mar 06 2017 14:45
Oh cool!
Paolo Di Tommaso
@pditommaso
Mar 06 2017 14:46
:v:
Isak Sylvin
@sylvinite
Mar 06 2017 14:46
The classpath-.. generated upon runtime, what environment variable dictates where it ends up?
Paolo Di Tommaso
@pditommaso
Mar 06 2017 14:47
do you mean where it is written ?
Isak Sylvin
@sylvinite
Mar 06 2017 14:48
Yes, sorry for the phrasing
Paolo Di Tommaso
@pditommaso
Mar 06 2017 14:48
NXF_LAUNCHER
Isak Sylvin
@sylvinite
Mar 06 2017 14:49
Thanks
Paolo Di Tommaso
@pditommaso
Mar 06 2017 14:49
you are welcome
Stian Soiland-Reyes
@stain
Mar 06 2017 16:42
Hi -- are there any recent thoughts or development on supporting CWL workflows with nextflow? We talked about "nextflow-as-cwl" being tricky, but running "cwl-in-nextflow" a bit more achievable.
Paolo Di Tommaso
@pditommaso
Mar 06 2017 16:43
Hi @stain, we have just started to explore the second option
Stian Soiland-Reyes
@stain
Mar 06 2017 16:44
oh very cool
have you looked yet at parsing CWL with Java?
Paolo Di Tommaso
@pditommaso
Mar 06 2017 16:45
that is going to be the next step, is there library out of there that could be useful ?
I mean CWL library . .
Stian Soiland-Reyes
@stain
Mar 06 2017 16:49

I'm afraid it's not too cool.. cwljava is a bit weird - particularly in how it's built :-(
our student ended up doing his own quick YAML deconstruct.
He's making a CWL viewer for the web.
CWL workflow

But there's also rabix-bindings-cwl which looks more promising - I must admit I've not tried to use it outside Rabix.

Paolo Di Tommaso
@pditommaso
Mar 06 2017 16:51
Thanks for the links, I will give a look though I'm expecting to parse the CWL file not so difficult with a good YAML library
or I'm missing something ?
cool the CWL viewer, is that open sourced ?
Stian Soiland-Reyes
@stain
Mar 06 2017 16:59
yes, of course! https://github.com/common-workflow-language/cwlviewer/ Apache License 2.0.
no, it's easy enough with a YAML library as my student did.. but you have to just map identifiers etc. yourself.
Paolo Di Tommaso
@pditommaso
Mar 06 2017 17:01
I see
Stian Soiland-Reyes
@stain
Mar 06 2017 17:02
and you have to handle the syntactic sugar.. like there's three different ways to declare an input port in CWL.
I wish I had time to get that cwljava in shape :-/
or a refresh
Paolo Di Tommaso
@pditommaso
Mar 06 2017 17:02
out of curiosity, do you have a specific need regarding the CWL support in NF ?
Stian Soiland-Reyes
@stain
Mar 06 2017 17:02
for a grant proposal..
I want to list Nextflow :)
Paolo Di Tommaso
@pditommaso
Mar 06 2017 17:03
ahah, I see
Stian Soiland-Reyes
@stain
Mar 06 2017 17:03
so I just say vaguely.. "under planning or development"
which is about the same as CWL in Apache Taverna - we did some already, but we're not there at running CWL yet
Paolo Di Tommaso
@pditommaso
Mar 06 2017 17:04
I'm wondering if it could have sense a common effort or even a collaboration?
Stian Soiland-Reyes
@stain
Mar 06 2017 17:23
yes please! :)
if you imported a CWL workflow in Nextflow somehow (converted or otherwise) - would it then be able to run on any of the Nextflow backends, you think?
or do some of them not like say Docker..
I mean.. would a CWL-nextflow workflow have to be hand-written for the particular backend in mind
Paolo Di Tommaso
@pditommaso
Mar 06 2017 17:39
well, the idea is to have CWL to NF tool that converts a CWL definition to a proper NF script
thus it should run on any backend supported by NF
Michael L Heuer
@heuermh
Mar 06 2017 23:40
@stain @pditommaso Nextflow + CWL + Apache Spark/ADAM is still something we're interested in, although haven't been able to find time to think about it recently. Has there been any thought to long-running services in CWL since the 1.0 release?