GENOMESCOPE module fails with exit 127 — genomescope.R not in container PATH (v1.1.0)

[vincentmanz]

Description of the bug

Bug description

The GENOMESCOPE process fails with exit status 127 (command not found) on every real run. The module script calls genomescope.R with positional arguments, but the specified container (quay.io/biocontainers/genomescope2:2.0--py311r42hdfd78af_6)
does not ship genomescope.R in $PATH — only the genomescope2 Python wrapper is present at /usr/local/bin/genomescope2.

This is not caught by stub-runs because stub mode never executes the script block.

Steps to reproduce

Run nf-core/genomeassembler v1.1.0 with ONT data (--ont) and default parameters. The pipeline fails at the NFCORE_GENOMEASSEMBLER:GENOMEASSEMBLER:ONT:JELLYFISH:GENOMESCOPE step for all samples.

Error message

.command.sh: line 2: genomescope.R: command not found

Exit status: 127

Container inspection

  apptainer exec quay.io-biocontainers-genomescope2-2.0--py311r42hdfd78af_6.img \
    find /usr /opt -name "genomescope*"
  # Returns:
  # /usr/local/bin/genomescope2          ← only this; no genomescope.R
  # /usr/local/conda-meta/genomescope2-2.0-py311r42hdfd78af_6.json
  # /usr/local/lib/R/library/genomescope/...

Root cause

modules/local/genomescope/main.nf line 22:

genomescope.R $histo $kmer_length $read_length genomescope

The genomescope2 conda package (build py311r42hdfd78af_6) no longer exposes genomescope.R as a standalone executable in $PATH. The Python wrapper genomescope2 is the correct entry point and accepts equivalent arguments via named flags, producing
the same output file structure.

Suggested fix

  - genomescope.R $histo $kmer_length $read_length genomescope
  + genomescope2 -i $histo -k $kmer_length -l $read_length -o genomescope

The mv commands downstream do not need changes — genomescope2 calls the same R code and produces identical output filenames (plot.png, plot.log.png, summary.txt).

Command used and terminal output

Relevant files

No response

System information

No response

[nschan]

You are correct that this container does not contain genomescope.R, however, the pipeline ships genomescope.R in bin/ and it is unclear to me why this does not work for you.

[github-actions]

This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days.

[github-actions]

This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity.