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  • Nov 16 13:37
    pditommaso commented #1276
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    pditommaso commented #69
  • Nov 14 14:57

    pditommaso on master

    Fix Allow the output of process… (compare)

  • Nov 14 14:48
    pditommaso edited #69
Paolo Di Tommaso
@pditommaso
well, datetime is a mess in any programing lang
Maxime Garcia
@MaxUlysse
It is?? I'll go check my tests then, I just tried and it wasn't working
Paolo Di Tommaso
@pditommaso
well, actually I'm not sure :joy:
Maxime Garcia
@MaxUlysse
It works
I must had another issue when I tried earlier
I'm guessing it'll work as well with s3://
Paolo Di Tommaso
@pditommaso
s3 can be traversed as a regular fs
Maxime Garcia
@MaxUlysse
Ok
thanks
Ashley S Doane
@DoaneAS
@rsuchecki thanks, yes pipeline is here: https://github.com/DoaneAS/realign.nf
Paolo Di Tommaso
@pditommaso
there could be something wrong in your script, NF is not supposed all that CPU
Daniel E Cook
@danielecook
@pditommaso agreed - but I'm curious why the groovy Date module doesn't work? Is it not imported?
Paolo Di Tommaso
@pditommaso
actually I'm not aware of it, therefore is not imported :smile:
is tehre a groovy-date module ?
Ashley S Doane
@DoaneAS
@rsuchecki pretty simple nextflow with only 1 process actually. Just takes a sampleindex.csv file with sample name, sample type (tumor or normal), and bam file path, and does a realignment with speedseq. The executor is sge, and the error seems to happen when nextflow is determining which results are cached.
Daniel E Cook
@danielecook
err maybe not - but the language spec suggests you should be able to do just Date.parse(format, input)
examples also present here: http://groovy-lang.org/single-page-documentation.html; Just curious maybe I'm missing something here
Paolo Di Tommaso
@pditommaso
can't check now, you may wont to report an issue
Daniel E Cook
@danielecook
I can do that
thanks
Paolo Di Tommaso
@pditommaso
welcome
Maxime Garcia
@MaxUlysse
OK, so I made a mistake earlier, it is not working in fact
I'll make a minimal example and an issue
Sri Harsha Meghadri
@harshameghadri
Hey folks, I am pretty new to using docker and singularity. I want to use the nf-core/rnaseq for my analysis. I consistently get errors while trying to execute this command singularity pull --name nf-core-rnaseq-1.3.img docker://nf-core/rnaseq:1.3
Unable to pull docker://nf-core/rnaseq:1.3: conveyor failed to get: Error reading manifest 1.3 in docker.io/nf-core/rnaseq: errors:
I am trying to pull to rackham. My analysis needs to be executed on bianca. Any tips are super appreciated.
Maxime Garcia
@MaxUlysse
try singularity pull --name nf-core-rnaseq-1.3.img docker://nfcore/rnaseq:1.3 instead, without the - in nf-core
I'm guessing if you have more question about nf-core pipelines, it should be better on our slack: https://nf-co.re/join
Sri Harsha Meghadri
@harshameghadri
I tried that as well getting the same error @MaxUlysse
Maxime Garcia
@MaxUlysse
You tried that on bianca?
Sri Harsha Meghadri
@harshameghadri
nope on rackham, I guess it needs internet
Maxime Garcia
@MaxUlysse
Sure
Just trying to find an easy mistake, sorry ;-)
Have you tried running that on an interactive node?
Sri Harsha Meghadri
@harshameghadri
hmmm on rackham? I dnt have allocation there.
Maxime Garcia
@MaxUlysse
I'm afraid singularity might be too demanding on the regular login node
Let me see if I can help you in an other way
Sri Harsha Meghadri
@harshameghadri
perfect, thank you Maxime.
Maxime Garcia
@MaxUlysse
@harshameghadri I messaged you ;-)
Marko Melnick
@Senorelegans
Is there any way to force a process to wait for another process to finish before it is started? I tryed to do it with a dummy channel but I am concatenating files to the channel amounts change from one process to the next.
Maxime Garcia
@MaxUlysse
can't you use the output from the process that need to be finished as an input for the other?
maybe with a .collect() to be sure to catch multiple executions of said process
Marko Melnick
@Senorelegans
I am concatenating fastq files by groups (I made a parser in groovy to separate by group). Is there no way to just make one process wait for another one with a dummy channel or some null variable?
I guess my real issue is I am reading channels from pairs earlier. And I have a list of the file name with condition group in a sample table that I can read, but I am struggling bringing them and operating on them by group.
Stijn van Dongen
@micans
@Senorelegans can you make a functioning toy example that illustrates your issue? Grouping is usually done by groupKey -> transpose -> groupTuple; e.g.
Channel.from(['a', [1, 2, 3]], ['b', [4, 5]], ['c', [6, 7, 8]])
   .map { tag, stuff -> tuple( groupKey(tag, stuff.size()), stuff ) }
   .view()
   .transpose()
   .map { tag, num -> [tag, num*num+1 ] }
   .view()
   .groupTuple()
   .view()
Ashley S Doane
@DoaneAS
@rsuchecki any ideas on this issue with java cpu use when nextflow is reading the results cache following nextflow -resume? I’m running nextflow on plenty of available resources (192 CPUs, 10T ram), but I’ll try submitting nextflow command as a job. This way SGE will kill it if CPU usage is too high.
Ashley S Doane
@DoaneAS

Also, I had the

executor {
    queueSize=1000
}

But thinking more about how sge works, this is not necessary (jobs are not run based on how long they have been in queue, but based on job priority that SGE determines and updates). Seems possible that this setting coild have caused an issue.

Anthony Ferrari
@af8
Hi all, is it possible to have publishDir directive to resolve symlinks in move mode ? I have a folder going from a process to another, I modify its content in the second process and publish it. But what is actually published is the symlink to the first process workdir. I would like it to be moved physically. Thanks
Rad Suchecki
@rsuchecki
A few ideas @DoaneAS - but I am not convinced by any of them... here is a couple
  • If the problem persists try to look into JVM settings regarding memory and GC - which could be the cause - but why would there be that much garbage to collect in the first place?
  • IO - NF process having to shift all the result files to publishDir - again there is not that many of them so not sure this could be the issue but you could disable publishDir in the first place to see if it makes a difference and re-enable in another run with -resume to publish the cached results.