These are chat archives for nextflow-io/nextflow

Apr 2019
Paolo Di Tommaso
Apr 25 05:30
This a know problem see here
that check needs to be improved but real issue is that the job fails during the submission
you are using slurm as well, right?
Steve Marshall
Apr 25 05:46
I'm trying to launch some jobs via AWS Batch which works fine however I need to ensure there is sufficient space inside the container for downloading large files. I have an AMI that has a mounted drive 250GB under /scratch I've configured the job definition to map that host volume to a container volume... but it doesn't seem like docker is using that volume and my nextflow task is running under /tmp/...
Paolo Di Tommaso
Apr 25 05:54
so far, it's only possibile using your own JobDefinition
Pierre Lindenbaum
Apr 25 06:20
@pditommaso yes it's a wrapper over slurm.
@pditommaso do you think there is anything I could quickly implement in my custom executor ? what would be the best place in the code to implement this ? Thanks.
Paolo Di Tommaso
Apr 25 10:43
it should be possible improving the GridTaskHandler#checkIfRunning logic, so that it also check the job status in the cluster somehow similar to how is done here
Adrian Viehweger
Apr 25 14:21
say I create an assembly from some Illumina paired reads, and want to map some Nanopore data to this assembly. I want to do this for several samples. how can I ensure nextflow coordinates the right assembly with the corresponding Nanopore reads?
Sinisa Ivkovic
Apr 25 16:51
Hi @pditommaso , I have a quick question concerning resume function Would -resume work if you copy work directory to another location? I tried that and I get WARN: It appears you have never run this project before -- Option -resume is ignored, so I just wanted to check is this expected behavior?