These are chat archives for nextflow-io/nextflow

20th
Feb 2019
Laurence E. Bernstein
@lebernstein
Feb 20 02:15
You guys are really helpful BTW. Thanks.
Got another question.. Docker executable containers are going to be deprecated, so what is the replacement syntax/method?
Qi ZHAO
@likelet
Feb 20 02:44
what do you mean " Docker executable containers are going to be deprecated" ? is there something wrong with the docker ?
i just joined in this chat yesterday, did you guys discuss this before?
Qi ZHAO
@likelet
Feb 20 03:11
get, thanks !
Paolo Di Tommaso
@pditommaso
Feb 20 10:40
there's not supposed to be replacement for executable containers, it was an experiment but it turned out not so useful and above the industry standard (read Kubernetes, AWS batch, etc) are not supporting them
Michael Epstein
@miepstei
Feb 20 13:21

Hi, I have a quick question behind channel.create(). I'm trying to create a channel and mix channel emissions into it. When I create a channel and mix channels into it, the nextflow process does not finish. I've tried adding .close() to terminate the channel but it doesn't work. Consider

c1 = Channel.from( 1,2,3 )
c2 = Channel.from( 'a','b' )
c3 = Channel.from( 'z' )

c1.mix(c2,c3).subscribe{println (it)}

versus

channelObj = Channel.create().mix(c1, c2, c3).close()
channelObj.subscribe{println (it)}

In the latter case I'm finding the output is

NXF_VER=19.01.0-edge nextflow run test.nf
N E X T F L O W  ~  version 19.01.0-edge
Launching `test.nf` [scruffy_wilson] - revision: 8252cbc92d
1
2
3
a
b

and the process doesn't terminate

Paolo Di Tommaso
@pditommaso
Feb 20 13:25
forget it, will be deprecated soon
Michael Epstein
@miepstei
Feb 20 13:26
okey-cokes. Thanks @pditommaso
Paolo Di Tommaso
@pditommaso
Feb 20 13:26
:+1:
Guillaume Theaud
@GuillaumeTh
Feb 20 14:07
Hi, I would like to create channels from a json file. Do you have an example to do that ? Currently I use subscribe and inside I create my lists but I can't do a Channel with them after.
Caspar
@caspargross
Feb 20 14:36
is there a way to start nextflow with a custom runName ("friendly_pesquet") ? I want the runNames to be identical to the name of my output folders.
Toni Hermoso Pulido
@toniher
Feb 20 15:43
Hi, I have a pipeline with a process (attached to the root, not dependent on any previous process) with a low maxForks numbers and I have noticed it always waits for other processes that are not prerequisite to finish. Why could this be happening?
Paolo Di Tommaso
@pditommaso
Feb 20 15:57
local computer ?
Toni Hermoso Pulido
@toniher
Feb 20 15:57
no, Univa, at CRG
Paolo Di Tommaso
@pditommaso
Feb 20 15:58
don't know
Clément ZOTTI
@czotti
Feb 20 16:16
Did you have any insights on why the -process.clusterOptions '--exclude=node[01-02],node_test' is not added in the .command.run when given as command line argument (using SLURM).
For every other solutions, inside the process it's working, and inside nextflow.config it's working also.
Paolo Di Tommaso
@pditommaso
Feb 20 16:16
nope
Clément ZOTTI
@czotti
Feb 20 16:19
Is it intended to work or more like undefined behavior ?
Paolo Di Tommaso
@pditommaso
Feb 20 16:19
it may happen something weird here
Clément ZOTTI
@czotti
Feb 20 16:19
ok
Paolo Di Tommaso
@pditommaso
Feb 20 16:20
it's possible the --something is parsed as a number
Clément ZOTTI
@czotti
Feb 20 16:21
Oh that's quite unfortunate, thanks for the answer.
Maxime Garcia
@MaxUlysse
Feb 20 18:58
@pditommaso Congrats for the subworkflow
Looks quite exciting
Paolo Di Tommaso
@pditommaso
Feb 20 20:29
:v:
still a lot of work tho
Alexander Peltzer
@apeltzer
Feb 20 20:29
Still congrats tho ;-)
Looks really exciting :-)
Paolo Di Tommaso
@pditommaso
Feb 20 20:30
there's a lot of space for improvement and explore new ideas
Laurence E. Bernstein
@lebernstein
Feb 20 20:30
I would really LOVE to have subworkflows. Are they available yet?
Paolo Di Tommaso
@pditommaso
Feb 20 20:31
@apeltzer looking forward to discuss with you guys in tubingen
@lebernstein on going dev nextflow-io/nextflow#984
Alexander Peltzer
@apeltzer
Feb 20 21:12
Looking forward too 👍
evanbiederstedt
@evanbiederstedt
Feb 20 21:31
Question: we're creating a mock to test the scale of jobs/executions with Nextflow---just to be clear, what are the API calls Nextflow uses to submit jobs to AWSBatch? Could you explain this a bit more?
evanbiederstedt
@evanbiederstedt
Feb 20 21:36
The idea is to see how nextflow deals with 10K jobs at once :)
Laurence E. Bernstein
@lebernstein
Feb 20 22:48
Looking ahead, I am interested in whether it makes a difference if one submits 100 separate workflows or 1 workflow with 100 samples when using Kubernetes. Unfortunately I currently don't currently have a Kube installation to test such a thing.