[Microarray] Issue creating cache directories in quarto render command for updated Nextflow version

[cyouh95]

Description

No issues when using Nextflow v.22.10.0.5826, but after updating to Nextflow v.23.10.1.5891, the following error arose in AGILE1CH / PROCESS_AFFYMETRIX processes from quarto render command:

Could not create TypeScript compiler cache location: "/home/<user>/.cache/deno/gen"
  Check the permission of the directory.

According to here, this cache location can be changed using environment variable DENO_DIR.

That resolves this issue, but a second error follows:

Uncaught Error: Read-only file system (os error 30), mkdir '/home/<user>/.cache/quarto'

For both cache directories, they seem to be put by default inside the user's home directory. This suggests setting HOME env var to a temp directory. This would cover the first issue too without the need to separately specify DENO_DIR.

Solution

Set HOME to be the working directory inside AGILE1CH / PROCESS_AFFYMETRIX processes:

export HOME=$PWD;

The result is the cache directories will both appear inside the working directory within work/ folder:

work/<hash>/
|- .cache/
  |- deno
  |- quarto