nf-core/Lobby

We have moved over to slack, get your invite here (!): http://nf-core-invite.herokuapp.com and visit us https://nfcore.slack.com

Paolo Di Tommaso

@pditommaso

KochTobi

@KochTobi

Manage passwords ...

Sven F.

@sven1103

omg

Paolo Di Tommaso

@pditommaso

this think they have a different password for each channel I will never digest ..

Sven F.

@sven1103

yeah, this is kind of annyoing

Paolo Di Tommaso

@pditommaso

should I launch a nextflow channel on spectrum .. :satisfied:

Sven F.

@sven1103

huh, don't know this one

Phil Ewels

@ewels

That’s the one that’s just been bought by GutHub right?

@pditommaso - this is why I use the slack clients though! Keeps all of the different organisations together easily. Only need to do it once on mobile and once on desktop :)

Paolo Di Tommaso

@pditommaso

That’s the one that’s just been bought by GutHub right?

yep !

this is why I use the slack clients though

nice, to not sure I want another source of distraction ! :satisfied:

Qi ZHAO

@likelet

hi, a simple question. Why the $workDir in config file can not be recognized by NF

N E X T F L O W  ~  version 19.01.0
Launching `RNAseqPipe/main.nf` [thirsty_hamilton] - revision: a2f41a936f
This workflow requires Nextflow version 0.26 or greater -- You are running version 19.01.0
ERROR ~ GTF file not found: $workDir/Genome/gencode.chr22.gtf

 -- Check '.nextflow.log' file for details

seems paste the wrong place again ...

Pontus Frehult

@pontus

Hi all, I'm trying to help NGI Sweden debug an issue where 19.01.0 incorrectly thinks slurm jobs are gone and give up, but am not sure how much farther I'm gonna get without some tips.

I've gotten down to checkActiveStatus in ./modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy

Feb-27 08:46:35.309 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > map does not contain jobId: 557670

but I also have an strace for this controller run, and have lines like

30833 write(1, "557514 CD\n557315 CD\n557670 R\n557671 R\n", 38 <unfinished ...>

for all the invocations of squeue (any attempt to get queue status that has gotten so far as execv). I also see corresponding read lines.

For some of these I see

Feb-27 08:38:55.328 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > cmd exit: 0
557514 CD
557315 CD
557670 R
557671 R

Feb-27 08:38:55.335 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status >
job: 557514: DONE
job: 557315: DONE
job: 557670: RUNNING
job: 557671: RUNNING

which is fine, but I also see quite a few

Feb-27 08:39:55.354 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > cmd exit: 0

Feb-27 08:39:55.355 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status >
(empty)

leading up to

Feb-27 08:39:55.355 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > map does not contain jobId: 557670

Any tips on getting further with this?

Paolo Di Tommaso

@pditommaso

this should be reported in the NF project https://github.com/nextflow-io/nextflow/issues

Paolo Di Tommaso

@pditommaso

actually I think it's related to this nextflow-io/nextflow#1045

Alexander Peltzer

@apeltzer

Also we’ve moved to slack in nf core :-)

Paolo Di Tommaso

@pditommaso

I guess he confused it for NF channel

Alexander Peltzer

@apeltzer

Yes :-)

Phil Ewels

@ewels

I wonder if we should close this chat group to avoid future confusion... :/

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.

Alexander Peltzer

@apeltzer

Yes - makes sense, alreay put up the info in the header too

sureshhewa

@sureshhewabi

Can nextflow log file location customized by passing as a params?

Alexander Peltzer

@apeltzer

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:

Phil Ewels

@ewels

Also this is for nf-core, not to be confused with the gitter channel for nextflow itself: https://gitter.im/nextflow-io/nextflow

Michael L Heuer

@heuermh

@apeltzer Considering moving back to Gitter? I didn't come with because Slack disagrees with me.

Phil Ewels

@ewels

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

@heuermh

@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!

Phil Ewels

@ewels

Ok, understandable. There's always tools like https://slackdigest.com/ ;) But yes - there should be a few people at BOSC / CoFest / ISMB..

RationalTangle

@RationalTangle

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

Alexander Peltzer

@apeltzer

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:

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

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