@apeltzer Considering moving back to Gitter? I didn't come with because Slack disagrees with me.
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.
Michael L Heuer
@ewels I'm spread across too many projects for Slack to be workable on a daily basis. With Gitter there is good Github integration and it's not too unreasonable to follow many different projects. I'll try to catch up with nf-core at BOSC and/or the CoFest!
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
You found the Slack already @RationalTangle ;-) Either there or open an issue on GitHub in the nf-core/rnaseq repository :-)
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
both JAVA_CMD and HOME directories are correct
problem solved there was a problem with the gawk installation