These are chat archives for nextflow-io/nextflow

22nd
Apr 2018
Ashley S Doane
@DoaneAS
Apr 22 2018 21:28
hi @pditommaso and others that might be using sge executor... I noticed that nextflow is setting the 'virtual_free' option in the the qsub script. Is there a way I can tell nextflow to omit this? It causes some problems on our cluster and jobs won't get scheduled if that option is defined. We use "h_vmem [mem per cpu]", and I just set this in cluster options like cluster options '-l h_vmem=5G'
Diogo Silva
@ODiogoSilva
Apr 22 2018 21:28
Are there any updates on the interactive command line tool that's mentioned in the GH projects page (https://github.com/nextflow-io/nextflow/projects/1)? I would be really nice to have some way of checking the progress of a pipeline run, specially for large data volumes where one quickly loses track :smile:
Ashley S Doane
@DoaneAS
Apr 22 2018 21:30
also, is it possble I am doing something inadvertently to cause 'virtual free' to be set? thanks :)
Ashley S Doane
@DoaneAS
Apr 22 2018 22:48
@vsmalladi thanks, just saw this. Great idea- I use IDR a lot but haven't integrated into the nextflow pipeline. I call it with bash scripts, so it would be pretty simple to set up, would just add a variable in the samples.csv file to indicate replicates. I'll work on it when I havea chance....