These are chat archives for nextflow-io/nextflow

15th
Jun 2017
Shellfishgene
@Shellfishgene
Jun 15 2017 07:32
@ewels I didn't even realize StringTie actually outputs counts, that's what you use for further processing I assume?
Phil Ewels
@ewels
Jun 15 2017 11:13
StringTie does normalised values, we use featureCounts to output raw counts I think..
Shellfishgene
@Shellfishgene
Jun 15 2017 11:38
STAR, HISAT, kallisto, salmon; RSEM, stringtie, featureCounts, htseq_count; EdgeR, Deseq2, ballgown, sleuth. Too many options nowadays...
Shellfishgene
@Shellfishgene
Jun 15 2017 14:05
@pditommaso What could be a reason nf does not resume a pipline? I have one for assembling a few samples, and had resumed it twice for missing samples 2 weeks ago, that worked fine. Now I want to run it again with one additional sample, but nf submits processes for all of them again. I have not changed the nf script at all.
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:40
May it be that u relaunched once without resume? In that you be last the resuming session
*lost
Shellfishgene
@Shellfishgene
Jun 15 2017 14:40
Hmm, I don't think so. Any way to get the last resumeable session back?
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:41
Try nextflow log to see all launched instances
Yes, it's in the log
Shellfishgene
@Shellfishgene
Jun 15 2017 14:47
It looks no pipeline was executed in this folder hmm...
where would that inf come from? the .nextflow dir ist there.
But empty. Must be a problem on my side the I guess...
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:48
Umm yes
Something may it be deleted the content of that folder?
Shellfishgene
@Shellfishgene
Jun 15 2017 14:49
Weird, the work dir is there with the data, the nextflow logs are all there. I certainly did not delete just the content of .nextflow
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:50
No idea, that folder contains the executions history
Shellfishgene
@Shellfishgene
Jun 15 2017 14:51
I just started netxtflow and pressed ctrl-c to stop it when I saw it resubmitted all the old jobs. Does it remove the history info then?
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:52
No
Shellfishgene
@Shellfishgene
Jun 15 2017 14:52
But it should have written something into .nextflow?
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:52
But won't delete it
The NF command that delete that diirs
*dirs
Is nextflow clean
Shellfishgene
@Shellfishgene
Jun 15 2017 14:54
I just ran netxtflow again as before, now the cache dir is there. Weird.
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:55
Is a shared folder?
Shellfishgene
@Shellfishgene
Jun 15 2017 14:55
No...
Paolo Di Tommaso
@pditommaso
Jun 15 2017 14:56
Super weird
Shellfishgene
@Shellfishgene
Jun 15 2017 14:57
We sometimes have filesystem problems, maybe it was something like that.
Paolo Di Tommaso
@pditommaso
Jun 15 2017 15:04
.nextflow must contain two directories cache and history
Shellfishgene
@Shellfishgene
Jun 15 2017 15:05
yes, it does now
No idea, I'll look into it when it happens again...
For now I'll blame the NEC filesystem that nobody uses but us. And maybe someone in Japan.
Paolo Di Tommaso
@pditommaso
Jun 15 2017 15:06
:)
Shellfishgene
@Shellfishgene
Jun 15 2017 15:08
nf prints [a8/25d859] Submitted process to stdout, can I make it also print if a process is finished?
Paolo Di Tommaso
@pditommaso
Jun 15 2017 15:09
Umm maybe there's something ilikr that in the log file
Shellfishgene
@Shellfishgene
Jun 15 2017 15:14
I guess it's not important anyway
bioinfo-geekz
@bioinfo-geekz
Jun 15 2017 17:09
Hi Nextflow users. I've been using it for a while and I like it a lot. But I have one problem with work directories and my quota in the cluster gets full fast.
Is there a way to organise or recycle my work directories?
Evan Floden
@evanfloden
Jun 15 2017 17:36
Hi @bioinfo-geekz Thanks for the compliments. If you need to "clean up" your work directories you can use:
nextflow cleanup
This will effectivly remove your the intermediate files. We are working on some more sophisticated ways to manage work directories at the moment :wink: