These are chat archives for nextflow-io/nextflow

3rd
Oct 2018
Bioninbo
@Bioninbo
Oct 03 2018 09:38
Hello Paolo, everybody,
I was wondering: Is it possible to specify that we want one process to be performed in priority (in case multiple processes have available input)? This would be very useful for developing purposes. For now I use when: do.processx but it is not convenient.
Luca Cozzuto
@lucacozzuto
Oct 03 2018 09:39
Hi all. I know that is not strictly related to nextflow but blast can be part of many bioinformatic workflows... https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty833/5106166
Paolo Di Tommaso
@pditommaso
Oct 03 2018 11:28
@Bioninbo no
Bioninbo
@Bioninbo
Oct 03 2018 11:57
Ok, I thought so but just wanted to be sure. Thanks @pditommaso
Maxime Garcia
@MaxUlysse
Oct 03 2018 11:59
I'm guessing you can force it, by using an output from this process as an input in other processes
Anthony Underwood
@aunderwo
Oct 03 2018 15:38
@pditommaso Does the latest release contain the -resume improvements to ignore time stamps?
Paolo Di Tommaso
@pditommaso
Oct 03 2018 15:40
Anthony Underwood
@aunderwo
Oct 03 2018 15:42
Thanks I'll try that out. I have a workflow that is not resuming correctly with all files stored on local SSD
Paolo Di Tommaso
@pditommaso
Oct 03 2018 15:42
ok, let me know
community! star your fav workflows on Dockstore
I don't have to say which ones :)
Winni Kretzschmar
@winni2k
Oct 03 2018 16:06
Is there a command line switch to turn on a specific type of caching for the whole pipeline? Alternatively, I assume one could set caching through the config file?
Anthony Underwood
@aunderwo
Oct 03 2018 17:02
Unfortunately lenient doesn't seem to help with the resuming thing
I run pipeline with -resume and it starts some completed jobs
I cancel with ctrl-C and rerun and after several attempts then resumes as it should do
Mike Smoot
@mes5k
Oct 03 2018 18:40
Wasn't a notification hook added for workflow.onComplete recently? This suggests not, but I'm pretty sure something was added. Assuming something was added, was there also a cleanup hook added? e.g. for removing the work dir?
Evan Floden
@evanfloden
Oct 03 2018 19:26
@winni2k Check out profiles. Should be able to provide all your config possibilities with a single flag
Paolo Di Tommaso
@pditommaso
Oct 03 2018 21:11
@mes5k maybe this ?
Mike Smoot
@mes5k
Oct 03 2018 21:18
Yes, I knew there was something! Thanks!
Mike Smoot
@mes5k
Oct 03 2018 21:26
I've got a function that we use in our pipelines that calls groovy's File.deleteDir to recursively deletes a directory, in our case to cleanup the work dir. However, it turns out that File.deleteDir also follows symlinks and deletes the original file. This was causing problems with files cached with storeDir and was wondering if (and hoping that) this is something others have encountered and solved.