These are chat archives for nextflow-io/nextflow

9th
Nov 2017
Edgar
@edgano
Nov 09 2017 08:26
Good morning,
Paolo Di Tommaso
@pditommaso
Nov 09 2017 08:26
morning
Edgar
@edgano
Nov 09 2017 08:28
Dummy question. If I run NF in my local machine, it will fail in some files due the low memory of my localbost. If I re-run it in the cluster with the -resume, will it work ? Or it will re-run all the files again?
Paolo Di Tommaso
@pditommaso
Nov 09 2017 08:29
it cannot, because the work dir files are in your computer .. which is not accessible from the cluster (I guess)
Edgar
@edgano
Nov 09 2017 08:31
Ok, it was what I was thinking... Thanks!
Rickard Hammarén
@Hammarn
Nov 09 2017 12:34

Hmm...

ERROR ~ Error executing process > 'multiqc (null)'
Caused by:
  Process `multiqc` is staging two or more input files with the same name -- offending files: stringtie/.command.log, rseqc/log.txt

those offending files don't seem to have the same name..?
https://travis-ci.org/SciLifeLab/NGI-RNAseq/builds/298050472

seems to be a 0.26 problem
Paolo Di Tommaso
@pditommaso
Nov 09 2017 12:36
it caused by nextflow-io/nextflow#470
this is a sanity check, different files staged with the same name are not allowed
is it possible that the multiqc process is saving both stringtie/.command.log, rseqc/log.txt with the same name?
Rickard Hammarén
@Hammarn
Nov 09 2017 12:40
yeah, I mean there should be a rseqc/log.txt per sample and a tringtie/.command.log per sample, a long with the logs from all other processes as well
Paolo Di Tommaso
@pditommaso
Nov 09 2017 12:41
can you provide me a link to that code ?
Paolo Di Tommaso
@pditommaso
Nov 09 2017 12:45
Um weird, that should be allowed. Could you open an issue for that?
Rickard Hammarén
@Hammarn
Nov 09 2017 12:46
Sure
Paolo Di Tommaso
@pditommaso
Nov 09 2017 12:47
thanks
Paolo Di Tommaso
@pditommaso
Nov 09 2017 13:01
@Hammarn you reminded me the need to add a simpler operator for debugging channels nextflow-io/nextflow#517
this could replace the pattern that I saw usually in your code
if ( condition ) {
  channel = channel.view()
}
with
channel.dump(tag:'foo')
Rickard Hammarén
@Hammarn
Nov 09 2017 13:03
Cool, seems useful. Glad to be of use :smile:
Tim Diels
@timdiels
Nov 09 2017 16:27
How would you do a full outer join of 2 channels?
I was thinking of a cross with onComplete somehow 'yielding' those from left/right which haven't been yielded yet
Tim Diels
@timdiels
Nov 09 2017 16:34
oh, phase is what I need
Is there any difference between cross and phase other than phase allowing for a remainder?
Paolo Di Tommaso
@pditommaso
Nov 09 2017 20:05
have a look at join operator