These are chat archives for nextflow-io/nextflow

Mar 2019
Oleksandr Moskalenko
Mar 02 03:37
@pditommaso I just remembered the reason for the bus error with nextflow. It happened on a lustre filesystem for a group that was above the soft quota, but still well below the hard quota limit and still within a grace period. In the end the solution was to get under the soft quota. Perhaps nextflow does a disk space check and could not tell that the user could still write to the filesystem.
Mar 02 03:58
Thank you, this is helpful!
Anthony Ferrari
Mar 02 13:46
Can a enc
Can a env and conda scopes be mixed in a profile ?
    standard {
        // Using a native version of 'tool'
        env {
            PATH = "/home/anthony/sw/tool:${PATH}"
        // Conda environment for other tools
        process {
             withName: 'do_stuff2' { conda = '/home/anthony/sw/miniconda2/envs/my-env-nf' }
I got an error that binaries in my-env-nf can not be found.
Paolo Di Tommaso
Mar 02 14:30
@sivkovic that's not correct, NF deletes all scratch files in the container, the container instead has to be removed by Batch