quarto/notebook: stop Quarto searching above the task directory for a project

[pinin4fjords]

What

When the task directory has no _quarto.yml, Quarto walks up the parent directories running its project-type detectors. An unreadable folder counts as "exists" (quarto-dev/quarto-cli#14980), so an ancestor containing an unreadable config/ and a content/ is taken for a Hugo project. Quarto then puts .quarto/ there and the render fails.

We hit this with nf-core/differentialabundance 2.0.0 on Seqera Platform with Fusion 2.5. There, /fusion/s3/config and /fusion/s3/content are other people's buckets, so every report failed with attempt to write a readonly database, including with -profile test. It can happen on any shared filesystem with unreadable entries above the work dir.

This writes project: { type: default } to _quarto.yml in the task directory before rendering, unless one was staged via input_files, so the search stops there.

Checked

• In the module's container (Quarto 1.7.31, x86_64), rendering a .qmd two levels below a folder with an unreadable config/ and a content/:
  • current script: .quarto is created in that ancestor, and the render fails (exit 1, no HTML);
  • with this change: .quarto is created in the task directory, and the HTML is rendered.
• nf-core modules test-equivalent nf-test test modules/nf-core/quarto/notebook --profile docker on x86_64: all 7 tests pass on master and on this branch, with snapshots unchanged.
• The same _quarto.yml workaround, applied through beforeScript, fixed differentialabundance 2.0.0 reports on Fusion 2.5.14.
• No new nf-test: reproducing needs an unreadable directory above the task's work dir, which the test sandbox can't set up.

PR checklist

• This comment contains a description of changes (with reason).
• nf-core modules test quarto/notebook --profile docker
• --profile singularity / conda: left to CI.

🤖 Generated with Claude Code

[heuermh]

Nice catch and fix!