Use $TMPDIR to set temporaryr directories

[Aratz]

HPC clusters typically specify the scratch area to be used with the environment variable TMPDIR. This PR makes sure we use it, and fallback on /tmp if it is not defined.

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• CHANGELOG.md is updated.

[johandahlberg]

I realized something about this. Is this evaluated at the processing node, or head node? I.e. if the tmpdir is set differently on each node we need to be sure this is set there, not at the head node.

[Aratz]

Good question! I couldn't find anything convincing enough in the docs, but I run the pipeline with the test profile and checked the .command.run file:

nxf_container_env() {
cat << EOF
export MPLCONFIGDIR="\${TMPDIR:-/tmp}/.config/matplotlib"
export NUMBA_CACHE_DIR="\${TMPDIR:-/tmp}/.numba_cache"
export XDG_CACHE_HOME="\${TMPDIR:-/tmp}/.cache"
export XDG_DATA_HOME="\${TMPDIR:-/tmp}/.data"
export PIXELATOR_DUCKDB_TEMP_DIR="\${TMPDIR:-/tmp}"
export PYTHONNOUSERSITE="1"
export R_PROFILE_USER="/.Rprofile"
export R_ENVIRON_USER="/.Renviron"
export JULIA_DEPOT_PATH="/usr/local/share/julia"
EOF
}

This is fed to the docker container when it is run, so this is run on the processing nodes.

[johandahlberg]

Ok. Than it should work as we want it to.