- If running on a virtual machine, you may need to set
export QT_QPA_PLATFORM="offscreen" for scanpy to work properly. Issue described here.
- We found Nextflow was writing some output into the
${HOME} directory. This resulted in a Java error as soon as a Nextflow command was executed. Based on file sizes within ${HOME}, it seemed like the output was being written within the conda environment (following du -h | sort -V -k 1). By deleting and re-installing the conda environment, the problem was solved. The below flags may help prevent this from the future. In addition, setting the flag export JAVA_OPTIONS=-Djava.io.tmpdir=/path/with/enough/space/ may also help.
# To be run from the execution dir, before the above nextflow command
# If you are running this on a cluster, make sure you log into an interactive
# session with >25Gb of RAM.
export NXF_OPTS="-Xms25G -Xmx25G"
export NXF_HOME=$(pwd)
export NXF_WORK="${NXF_HOME}/.nexflow_work"
export NXF_TEMP="${NXF_HOME}/.nexflow_temp"
export NXF_CONDA_CACHEDIR="${NXF_HOME}/.nexflow_conda"
export NXF_SINGULARITY_CACHEDIR="${NXF_HOME}/.nexflow_singularity"