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  • Jan 31 2019 22:52
    matq007 commented #261
  • Jan 31 2019 22:49
    matq007 edited #261
  • Jan 31 2019 22:46
    matq007 opened #261
  • Jan 31 2019 14:33
    ewels edited #252
  • Jan 31 2019 14:33
    ewels commented #252
  • Jan 31 2019 13:29
    pachiras commented #252
  • Jan 31 2019 12:34
    matq007 assigned #252
  • Jan 31 2019 11:53
    apeltzer commented #252
  • Jan 31 2019 10:51
    matq007 commented #252
  • Jan 31 2019 08:22
    apeltzer commented #252
  • Jan 31 2019 02:13
    pachiras commented #252
  • Jan 29 2019 20:42
    af8 starred nf-core/tools
  • Jan 29 2019 08:47

    nf-core-bot on api-doc

    Travis build: 816 (compare)

  • Jan 29 2019 08:42

    apeltzer on dev

    Markdown parsing: Fix all the e… Add new markdown rules to templ… Apparently whitespace isn't eno… and 2 more (compare)

  • Jan 29 2019 08:42
    apeltzer closed #260
  • Jan 28 2019 23:42
    ewels synchronize #260
  • Jan 28 2019 23:07
    ewels synchronize #260
  • Jan 28 2019 22:57
    ewels synchronize #260
  • Jan 28 2019 22:57
    ewels review_requested #260
  • Jan 28 2019 22:57
    ewels review_requested #260
Leon-Bichmann
@Leon-Bichmann
yld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib
Referenced from: /usr/local/bin/awk
Reason: image not found
ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later is installed
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
JAVA_CMD: /Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home/bin/java
JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home
both JAVA_CMD and HOME directories are correct
Leon-Bichmann
@Leon-Bichmann
problem solved there was a problem with the gawk installation
Combiz
@combiz_k_twitter
Hi if anybody could take a look at the question I posted on the google groups page that would be much appreciate: https://groups.google.com/forum/#!topic/nextflow/TnTxv4iMm88
Alexander Peltzer
@apeltzer
That might be a question for the nextflow channel
We also migrated to slack for Nf-core entirely
Combiz
@combiz_k_twitter
Thanks Alexander
Phil Ewels
@ewels
Yes, this is nf-core - the nextflow gitter channel is here: https://gitter.im/nextflow-io/nextflow
Combiz
@combiz_k_twitter
Is there a list anywhere defining 'nf-core best practices'? There's a lot going on in the template folder generated by nf-core create, a text description would be useful..
Phil Ewels
@ewels
Hello! Slack is better, nf-core Gitter is depreciated really (I should delete it..?)
But no, no description of the files in the template yet.
That’s a great idea!
If you could make an issue on the website repo, then we can definitely take a look into it
Or maybe as part of the documentation for the tools package..?
Combiz
@combiz_k_twitter
@ewels Thanks for the reply Phil, sure I'll add the issue on the repo
Jonathan Manning
@pinin4fjords

With apologies for the cross-posting from the Nextflow Gitter (hadn't actually twigged there was a separate nf-core channel):

I'm coming to the conclusion that running nf-core pipelines (at least out-of the box) on Kubernetes is a non-starter due to custom functions in the config file which don't play nice with k8s (according to previous statements by Paolo). Would anyone dispute that conclusion? Or am I missing an easy workaround? We're evaluating whether deploying the nf-core workflows this way is going to be feasible.

Specifically: if I run:

nextflow kuberun ebi-gene-expression-group/rnaseq -profile test,docker -v nextflow

(this is just the stock nf-core rna-seq workflow with a minor tweak to fix paths to assets), I get:

Unknown method `check_max` -- Did you mean?
  check_log

Exception in thread "Task submitter" groovy.lang.MissingMethodException: No signature of method: Script_5ee9b41e.check_max() is applicable for argument types: (Integer, String) values: [2, cpus]
Phil Ewels
@ewels
Hi @pinin4fjords - this Gitter is depreciated and not used any more
We keep it here to catch people such as yourself who are looking for something like it (though I often wonder if we should delete it)
Please ask on our slack org instead - see https://nf-co.re/join
Jonathan Manning
@pinin4fjords
Ahh good - I did ask there first, so I started in the right place. No clear solution though.
Phil Ewels
@ewels
:+1:
If it’s the check_max function that’s the problem, I guess you can just override the config files with a custom config that doesn’t use the function if you want though.
Bit of a hack / messy, but it’s a simple way to remove any reference to the function
Just copy + paste base.config from the pipeline, remove all check_max function calls and then use that config file with -c
Jonathan Manning
@pinin4fjords
Yes, can do that for specific cases- thank you. But I'm also interested if the general patterns of nf-core are compatible with k8s usage
Phil Ewels
@ewels
:+1:
I quite dislike this function so I hope we’ll be able to remove it in the future (we will probably have to with DSL2)