REPORT generation fails with tmpdir error in containerized environments

[wbau]

Description of the bug

Issue:

The REPORT process fails with ERROR: NotFound: No such file or directory (os error 2): tmpdir when running Quarto in Singularity containers.

Related Issues

This appears to be related to known Quarto-in-Singularity compatibility issues (see quarto-cli#2559)

Cause:

Quarto requires write access to temporary directories, but the containerised environment doesn't have them pre-created.

Minimal Working Solution:

Create necessary directories and set environment variables before running Quarto in modules/local/report/main.nf:

script:
"""
# Create necessary directories for Quarto in container
export HOME="\$PWD"
mkdir -p "\$HOME/.cache"
mkdir -p "\$HOME/tmp"
export TMPDIR="\$HOME/tmp"
export TEMP="\$TMPDIR"
export TMP="\$TMPDIR"

quarto render report.qmd \\
    --profile base,nanoq,quast,busco,jellyfish,merqury \\
     -P nanoq:true -P quast:true  -P busco:true -P jellyfish:true -P merqury:true \\
    --to dashboard
...
"""

Command used and terminal output

Relevant files

No response

System information

No response

[nschan]

Hello,

thanks a lot for reporting this issue and for providing a work-around. I will try to look into this soon.

[afonsoguerra]

I also found some issues with quarto and empty tabsets that I don't know if they are related to this or not, but in the end, it just needed quarto updated to the latest version, something to consider for the next release I guess.

[nschan]

@afonsoguerra This is a bit confusing. Empty tabsets should be the result of some parsing problem, and I am a bit surprised that updating quarto solved it.
I am currently contemplating if the current report format is worth the effort, or if the reporting should be done with multiqc instead. In any case, I will revisit the reporting as part of #171 and fix the issues mentioned here.

[afonsoguerra]

Thanks! Just for reference, here is the error I fixed with updating quarto. The original container used to reproduce the error is:
community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-89-8967e1cb830fdc77ec5b84541a50c74a0a05eaaae557314490809de2fc91e4af-data.img

Command executed:

  export HOME="$PWD"
  quarto render report.qmd \
      --profile base,quast,busco \
       -P quast:true  -P busco:true \
      --to dashboard
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:REPORT":
      R: $(R --version | head -n1 | sed 's/R version //; s/ .*//')
      r-tidyverse: $(ls /opt/conda/pkgs/ | grep tidyverse | sed 's/r-tidyverse-//; s/-.*//')
      r-plotly: $(ls /opt/conda/pkgs/ | grep plotly | sed 's/r-plotly-//; s/-.*//')
      r-quarto: $(ls /opt/conda/pkgs/ | grep r-quarto | sed 's/r-quarto-//; s/-.*//')
      quarto-cli: $(quarto --version)
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
      /opt/conda/lib/python3.13/site-packages/quarto_cli/share/formats/dashboard/template.html
    standalone: true
    section-divs: true
    html-math-method: mathjax
    wrap: none
    default-image-extension: png
    variables: {}
    
  metadata
    document-css: false
    link-citations: true
    date-format: long
    lang: en
    page-layout: custom
    title: nf-core/genomeassembler report
    author: ''
    editor: source
    nav-buttons:
      - icon: github
      - href: https://github.com/nf-core/genomeassembler
    
  Error running filter /opt/conda/lib/python3.13/site-packages/quarto_cli/share/filters/main.lua:
  ...thon3.13/site-packages/quarto_cli/share/filters/main.lua:21750: attempt to index a nil value (field 'tabs')
  stack traceback:
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:935: in function <...thon3.13/site-packages/quarto_cli/share/filters/main.lua:934>
  	(...tail calls...)
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:1152: in function <...thon3.13/site-packages/quarto_cli/share/filters/main.lua:1147>
  	(...tail calls...)
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:2943: in function <...thon3.13/site-packages/quarto_cli/share/filters/main.lua:2937>
  	(...tail calls...)
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:34: in upvalue 'run_filter_function'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:223: in function <...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:202>
  	(...tail calls...)
  	[C]: in function 'pandoc.List.map'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:202>
  	(...tail calls...)
  	[C]: in function 'pandoc.List.map'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:171: in upvalue 'recurse'
  	...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...o_cli/share/pandoc/datadir/../../filters/modules/jog.lua:202>
  	(...tail calls...)
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:572: in function <...thon3.13/site-packages/quarto_cli/share/filters/main.lua:550>
  	(...tail calls...)
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:1318: in local 'callback'
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:1336: in upvalue 'run_emulated_filter_chain'
  	...thon3.13/site-packages/quarto_cli/share/filters/main.lua:1372: in function <...thon3.13/site-packages/quarto_cli/share/filters/main.lua:1369>

[nschan]

Ok, thank you for sharing the error; this actually is not the kind of "empty tab" problem I was thinking of. Not sure if the root-cause is the same..