nextflow: fix long run with slurm

Nexflow requires userName, that is obtained from $USER.
The nix derivation somehows reset it.
Here we wrap nextflow command to force userName to $USER
at runtime.
This commit is contained in:
Alexis Praga 2025-07-09 23:05:40 +02:00
parent a64a649348
commit fec44452ab

View File

@ -87,7 +87,8 @@ stdenv.mkDerivation (finalAttrs: {
which
]
} \
--set JAVA_HOME ${openjdk.home}
--set JAVA_HOME ${openjdk.home} \
--set NXF_OPTS "-Duser.name=\''${USER}"
'';
passthru.tests.default = nixosTests.nextflow;