These are chat archives for nextflow-io/nextflow
Hi all, I often pass sets of values and files through channels connecting processes. For example
input: set(val(meta), file(data)) from someChannel
Occasionally, I want to apply one or more operator to the channel, which may result in what I believe is a set of sets (or tuple of tuples), but I don't think it is possible to then consume these like this:
input: set( set(val(meta1), file(data1)),set(val(meta2), file(data2))) from someChannel.anOperator().anotherOperator()
Am I missing some syntactic trick?
On a somewhat related note, it would aid code readability if the set notation could be used with input repeaters, for example:
input: each set(val(meta), file(data)) from someChannel
setdefinition cannot be nested, but this does not limit that ability to handle any n-tuple structure
CUDA_VISIBLE_DEVICESis not passed from SLURM to NF to Singularity. We've tried a bunch of things to pinpoint this and are preparing an NF issue atm
CUDA_VISIBLE_DEVICESand you need to access it, right?
CUDA_VISIBLE_DEVICESdepending on the available resources. It works via NF if we don't use Singularity. However, the environment variable is not set in the container itself.
env | sort
CUDA_VISIBLE_DEVICES=xxx bash .command.run
env | sortfor
.command.shthe content of this file is:
#!/bin/bash -ue echo $CUDA_VISIBLE_DEVICES
CUDA_VISIBLE_DEVICES=1 bash .command.runit print nothing.
CUDA_VISIBLE_DEVICES=xxx bash -x .command.run
WARNING: The maximum storage size of a single Docker container is by default 10GB, independently the amount of data space available in the underlying volume (see Base device size for more details).
Base Device Size