These are chat archives for nextflow-io/nextflow

4th
May 2018
Stephen Kelly
@stevekm
May 04 2018 02:23

not an API, but trace info and wf info on start/end/fail will be send via HTTP POST with a -with-messages option

hey I am trying it but getting the error:

Unknown option: -with-messages -- Check the available commands and options and syntax with 'help'
@sven1103
also do I have to run it from that repo directory? I tried to symlink to the launch.sh script from another location and it wouldnt work
Stephen Kelly
@stevekm
May 04 2018 03:24
nvm looks like you do have to run it from the parent directory and just pass the same args that you would to nextflow
Sendu Bala
@sb10
May 04 2018 08:45
Hi, looking at the code for the LSF executor, I can see stuff for parsing bjobs output and for doing bkill. But under what circumstances are those things used? Since nextflow stores its state on disk, does it need to check bjobs? When would it need to try and kill a job in LSF?
Sven F.
@sven1103
May 04 2018 08:57
@stevekm :+1: feel free to give me some feedback, the PR is ongoing now on #681
Paolo Di Tommaso
@pditommaso
May 04 2018 09:55
@sb10 it also uses bjobs to retrieve the current status and detect hang jobs
Sendu Bala
@sb10
May 04 2018 09:56
Would you expect any negative effects if bjobs didn't actually work, but all jobs end up being successful?
Paolo Di Tommaso
@pditommaso
May 04 2018 09:56
well yes, there could be negative side effects
why bjobs wont work ?
Sendu Bala
@sb10
May 04 2018 09:58
I'm writing an LSF "simulator" that nexflow can use, and just wondered if I had to fully simulate bjobs as well. I guess the answer is yes :)
Paolo Di Tommaso
@pditommaso
May 04 2018 09:58
oh, yes
Netsanet Gebremedhin
@gnetsanet
May 04 2018 19:13
Hello everyone. Can channels be created on the fly from within an input directive? I want to create a channel within a process so that dependency is properly established.
Paolo Di Tommaso
@pditommaso
May 04 2018 19:14
not sure to understand
Netsanet Gebremedhin
@gnetsanet
May 04 2018 19:19
input:
val(x) from Channel.fromPath("${barcodesOutputDir}/ANN_Outputs/**. mlmodel")
Paolo Di Tommaso
@pditommaso
May 04 2018 19:20
that's fine, tho you may need file(x) instead of val(x)
Netsanet Gebremedhin
@gnetsanet
May 04 2018 19:25
Thank you. So that is allowed. Nice!
Paolo Di Tommaso
@pditommaso
May 04 2018 19:25
:+1:
Netsanet Gebremedhin
@gnetsanet
May 04 2018 19:26
process collectAnnReports { 

 tag { "Collecting outputs" }

script:
Channel.fromPath("${barcodesOutputDir}/ANN_Outputs/**. mlmodel”).set {annOuts }


}
Paolo Di Tommaso
@pditommaso
May 04 2018 19:27
no, this makes no sense
Netsanet Gebremedhin
@gnetsanet
May 04 2018 19:27
Okay. it looks like annOuts will be out of scope?
I will stick with doing it in the input directive, then.