We have moved over to slack, get your invite here (!): http://nf-core-invite.herokuapp.com and visit us https://nfcore.slack.com
For future readers: Reminder that we have moved to Slack. See nf-co.re to get an invite (top right of any page) or visit https://nf-core-invite.herokuapp.com/ directly.
Reminder that we have moved to Slack. See nf-co.re to get an invite (top right of any page) or visit https://nf-core-invite.herokuapp.com/ directly.
:smile:
Also this is for nf-core, not to be confused with the gitter channel for nextflow itself: https://gitter.im/nextflow-io/nextflow
Not going to happen sorry @heuermh. There's too much discussion for gitter, it was impossible to keep track of the different threads. With slack we can have everyone in one place but split in to the different channels, also with threads in each channel. The difference has been huge.
We did have a look around at other solutions too, eg. Zulip and others. We didn't like them as much as Slack though..
What's wrong with Slack for you? I guess while we keep this gitter channel open we can always use both.. There's a mailing list too.
Ok, understandable. There's always tools like https://slackdigest.com/ ;) But yes - there should be a few people at BOSC / CoFest / ISMB..
I really appreciate the work you've all done already but is anyone interested in starting a conversation about how to add contaminant filtering/identification/visualization to the preprocessing pipeline of nf-core/rna-seq? It's a problem I'm currently dealing with and it feels like something that should be included in nf-core.
I know there are already old feature requests for adding salmon/kallisto and differential expression analysis, so I realize it might spread dev focus too thin
I'm new to nextflow, nf-core, and processing rna-seq data in general. Nevertheless, if my attempts to automate my own process could be folded into nf-core I'd be happy to help
Given how much questions / discussion points yuo have, maybe an issue to have the discussion streamlind would be a good start :+1:
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
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
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
We also migrated to slack for Nf-core entirely
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..?
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]
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
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
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)