These are chat archives for nextflow-io/nextflow

23rd
Sep 2015
Robert Syme
@robsyme
Sep 23 2015 05:14
I've got a workflow that finishes all of the steps including rendering the html timeline, but the nextflow process does not end. Is there a way of finding out what is preventing the nextflow process from finishing?
Paolo Di Tommaso
@pditommaso
Sep 23 2015 07:40
@robsyme could you please share with me the .nextflow.log file (maybe using pastebin or something like that)?
Paolo Di Tommaso
@pditommaso
Sep 23 2015 07:50
@robsyme you may try to put a return statement at line 171, resume the execution and verify if it stops
Robert Syme
@robsyme
Sep 23 2015 16:25
@pditommaso sorry for the slow reply. Adding a return at 171 results in the nextflow process stopping as expected. Log file is here
Paolo Di Tommaso
@pditommaso
Sep 23 2015 16:30
no pb, I guess you need to sleep from time to time ;)
that is the log for the one halting or the script where you put the return ?
Robert Syme
@robsyme
Sep 23 2015 16:33
The halting one.
Sorry the not halting one
Maybe I need more sleep ;)
Paolo Di Tommaso
@pditommaso
Sep 23 2015 16:34
:)
let me do some tests
Robert Syme
@robsyme
Sep 23 2015 16:40
Gar, sorry to be a pain! I thought that it might be something obvious that I was missing,
Paolo Di Tommaso
@pditommaso
Sep 23 2015 16:40
ok, I've found the problem
Robert Syme
@robsyme
Sep 23 2015 16:40
Ok that was fast.
Paolo Di Tommaso
@pditommaso
Sep 23 2015 16:41
it's this line
speciesNames.count().spread(alignments)...
actually there's bug in the spread operator that do not recognise correctly the termination of the count
Robert Syme
@robsyme
Sep 23 2015 16:42
It's a bit of a hacky way to do that anyway. I'll try and think of a better way of doing the filtering step.
Paolo Di Tommaso
@pditommaso
Sep 23 2015 16:42
well, it should work
I will fix it in the meanwhile you should be able to patch doing something like this
c = speciesNames.count().val
Channel.from(c).spread(alignments)...
Robert Syme
@robsyme
Sep 23 2015 16:43
That sounds sensible. Thanks!
Paolo Di Tommaso
@pditommaso
Sep 23 2015 16:44
welcome