These are chat archives for nextflow-io/nextflow

24th
Oct 2018
Maxime HEBRARD
@mhebrard
Oct 24 2018 05:24
hello, may I ask a naive question... why one channel is limited to only one subscriber/input ? I mean my representation of a flow would be to be able to branch any process(node) seamlessly ... but apparently I need to code each node and also each edge of my workflow manually :-/
Luca Cozzuto
@lucacozzuto
Oct 24 2018 07:24
@mhebrard can you post an example? I personally made channels resulting from merging / mixing / joining of many channels...
Maxime HEBRARD
@mhebrard
Oct 24 2018 07:37
Well I am reading more closely the doc and found about merging/mixing that should solve my problem and create "reusable output" ... sorry I am starting with nextflow and take me quite a hard time to wrape my head around the flow
Maxime HEBRARD
@mhebrard
Oct 24 2018 08:36
ok ... help needed: I have one file, I use splitCsv on it. then I want to run 2 process for each line ...
samples = Channel.fromPath(params.samplePath)
.splitCsv()
.subscribe{
  row -> //How do I create a channel to run a process for each row
}
Luca Cozzuto
@lucacozzuto
Oct 24 2018 08:41
samples = Channel.fromPath(params.samplePath)
.splitCsv().into{channelOne; channelTwo}
Maxime HEBRARD
@mhebrard
Oct 24 2018 08:48
thanks .. in the middle of experiment I get lost for simple stuff >.>
Luca Cozzuto
@lucacozzuto
Oct 24 2018 08:49
No prob : )
micans
@micans
Oct 24 2018 09:56
@pditommaso new console is awesome. Will it also be non-scrolling on resumption (so summary of cached tasks per-process)?
Luca Cozzuto
@lucacozzuto
Oct 24 2018 09:57
Now my turn :) I would like to make maxErrorRetry inside config file
    withLabel: little_comp {
        maxForks = 1
        maxErrorRetry = 2
    }
but I got
WARN: Unknown directive `maxErrorRetry` for process `msconvert`
micans
@micans
Oct 24 2018 09:58
maxRetries I know ...
Luca Cozzuto
@lucacozzuto
Oct 24 2018 10:00
mmm I mixed it with this...
micans
@micans
Oct 24 2018 10:04
I wondered about that
micans
@micans
Oct 24 2018 12:48

I have a general question about design. I have a pipeline that looks like 'Y'; say processess 1->2->3->4 and then 4->5->7->9 and 4-6->8->10 are two possible continuations depending on a command line parameter, so either I take one direction, or the other direction, but in a single running instance it will always be the same. As I understand it, I need to create empty channels, e.g.

if (params.studyid > 0) {
    ch_fastqs_dir = Channel.empty()
    process irods {
    ...

Is there another way to go about this? If I need to create empty channels for all channels in the other branch, it becomes less readable. Perhaps some scoping could be introduced, where a set of processes are known to interact only with each other and channels are local to that scope? Ready to hide behind a :door:

Maxime Garcia
@MaxUlysse
Oct 24 2018 13:15
I don't think you really need that
You just need to specify that your process 5 is to happen only when your command line is defined
and your process 6 for the specific parameter
the 5->7->9 or 6->8->10 will then happen naturally by chaining the output and input channels from the processes
Have a look into the when declaration: https://www.nextflow.io/docs/latest/process.html#when
micans
@micans
Oct 24 2018 13:37
aaaaah. when:, of course. Thanks!
So the idea is two connect 4 to both 5 and 6 right? The when: will be checked for each task. Is the overhead negligible, I wonder.
Maxime Garcia
@MaxUlysse
Oct 24 2018 13:41
That would be the idea
micans
@micans
Oct 24 2018 16:04
:+1: :fireworks:
Nice, wishing you an excellent new stage in the NF journey
Luca Cozzuto
@lucacozzuto
Oct 24 2018 16:11
@pditommaso congrats! Good luck with everything! Did you tell that Microsoft is going to buy NF? :joy: :joy: :joy: :joy:
chdem
@chdem
Oct 24 2018 16:18
@pditommaso This is good news !
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:21
@lucacozzuto shhhhhh :wink:
chdem
@chdem
Oct 24 2018 16:21
Does anyone also have problems with the console?
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:21
what kind of ?
chdem
@chdem
Oct 24 2018 16:21
a java.util.concurrent.RejectedExecutionException
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:22
ummm.. which version ?
chdem
@chdem
Oct 24 2018 16:22
last one
but my collegue had the same error with the 0.32
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:23
please fill out a bug report with an example
chdem
@chdem
Oct 24 2018 16:23
first run is ok, the execption is thrown from the second one
ok
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:23
ouch
Alexander Peltzer
@apeltzer
Oct 24 2018 16:25
Nice @pditommaso ! Congrats :-)
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:25
thanks !
long awaited change
Luca Cozzuto
@lucacozzuto
Oct 24 2018 16:27
nextflow.png
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:34
Then XP version :joy: :joy:
Alexander Peltzer
@apeltzer
Oct 24 2018 16:39
Please don't do a ME version!
Paolo Di Tommaso
@pditommaso
Oct 24 2018 16:40
:satisfied:
Luca Cozzuto
@lucacozzuto
Oct 24 2018 16:47
I imagine the questions: "Are you sure you want to resume?" "click here if you want to resume"
and then...
Critical-Service-Failed-BSoD-windows-10.jpg
Félix C. Morency
@fmorency
Oct 24 2018 17:42
@pditommaso Gratz :confetti_ball: !
Paolo Di Tommaso
@pditommaso
Oct 24 2018 17:43
:v:
Félix C. Morency
@fmorency
Oct 24 2018 17:45
Do you have any plans for a more startup-friendly commercial support pricing?
Paolo Di Tommaso
@pditommaso
Oct 24 2018 17:45
more compare to this ? https://www.seqera.io/
Félix C. Morency
@fmorency
Oct 24 2018 17:50
Yes. 400Euro/month is a lot for a startup like ours.
Paolo Di Tommaso
@pditommaso
Oct 24 2018 17:54
let see if we can shape an offer depending your specific needs, please contact me trough seqera channels
Félix C. Morency
@fmorency
Oct 24 2018 17:55
:+1: