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 :-/
@mhebrard can you post an example? I personally made channels resulting from merging / mixing / joining of many channels...
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
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
}samples = Channel.fromPath(params.samplePath)
.splitCsv().into{channelOne; channelTwo}
thanks .. in the middle of experiment I get lost for simple stuff >.>
No prob : )
@pditommaso new console is awesome. Will it also be non-scrolling on resumption (so summary of cached tasks per-process)?
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`
maxRetries I know ...
mmm I mixed it with this...
I wondered about that
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:
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
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.
That would be the idea
:+1: :fireworks:
Nice, wishing you an excellent new stage in the NF journey
@pditommaso congrats! Good luck with everything! Did you tell that Microsoft is going to buy NF? :joy: :joy: :joy: :joy:
@pditommaso This is good news !
@lucacozzuto shhhhhh :wink:
Does anyone also have problems with the console?
what kind of ?
a java.util.concurrent.RejectedExecutionException
ummm.. which version ?
last one
but my collegue had the same error with the 0.32
please fill out a bug report with an example
first run is ok, the execption is thrown from the second one
ok
ouch
Nice @pditommaso ! Congrats :-)
thanks !
long awaited change
Then XP version :joy: :joy:
Please don't do a ME version!
:satisfied:
I imagine the questions: "Are you sure you want to resume?" "click here if you want to resume"
and then...
@pditommaso Gratz :confetti_ball: !
:v:
Do you have any plans for a more startup-friendly commercial support pricing?
more compare to this ? https://www.seqera.io/
Yes. 400Euro/month is a lot for a startup like ours.
let see if we can shape an offer depending your specific needs, please contact me trough seqera channels
:+1: