diff --git a/modules/nf-core/quarto/notebook/main.nf b/modules/nf-core/quarto/notebook/main.nf index 8a1bee7870ae..dc776fb4d7a8 100644 --- a/modules/nf-core/quarto/notebook/main.nf +++ b/modules/nf-core/quarto/notebook/main.nf @@ -64,6 +64,10 @@ process QUARTO_NOTEBOOK { export XDG_CACHE_HOME="./.xdg_cache_home" export XDG_DATA_HOME="./.xdg_data_home" + # Without a _quarto.yml here, Quarto searches parent directories for a project and can + # pick one outside the task (https://github.com/quarto-dev/quarto-cli/issues/14980) + [ -e _quarto.yml ] || printf 'project:\\n type: default\\n' > _quarto.yml + # Fix Quarto for Apptainer (see https://community.seqera.io/t/confusion-over-why-a-tool-works-in-docker-but-fails-in-singularity-when-the-installation-doesnt-differ-i-e-using-wave-micromamba/1244) ENV_QUARTO=/opt/conda/etc/conda/activate.d/quarto.sh set +u