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  • Jan 31 22:52
    matq007 commented #261
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  • Jan 29 20:42
    af8 starred nf-core/tools
  • Jan 29 08:47

    nf-core-bot on api-doc

    Travis build: 816 (compare)

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  • Jan 29 08:42
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    ewels review_requested #260
KochTobi
@KochTobi
always gets me....
Sven F.
@sven1103
nf-core was already taken
-.-
Paolo Di Tommaso
@pditommaso
ohh, that's why I was not able to login there :satisfied:
Screenshot 2018-12-04 at 20.53.26.png
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
:D
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
image.png
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