sylph wrapper doesn't sanitize file names appropriately

[scottcain]

Summary

The Galaxy sylph_profile wrapper can generate an invalid shell command when the input FASTQ dataset name contains parentheses. The job fails before sylph runs with a shell syntax error near (.

Tool/version

• Tool: sylph profile
• Tool ID: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0
• Galaxy: usegalaxy.org, Galaxy 26.1

Reproducer

Run sylph profile on a FASTQ dataset with a name like:

ERR15660424 Sequel II WGS reads (PRJEB97182).fastq.gz

Using cached GTDB database settings.

Observed behavior

The job fails immediately with:

tool_script.sh: line 23: syntax error near unexpected token `('

The generated command includes a symlink target derived from the dataset name:

ln -s '.../dataset_....dat' 'ERR15660424_Sequel_II_WGS_reads_(PRJEB97182).fastq.gz' && \
sylph sketch ERR15660424_Sequel_II_WGS_reads_(PRJEB97182).fastq.gz ...

The ln -s target is quoted, but the later sylph sketch argument is not, so the shell parses the parenthesis and fails.

Expected behavior

The wrapper should either quote the dataset-derived filename everywhere it is used, or use a sanitized internal filename that avoids shell-special characters.

Workaround

Renaming the dataset to remove spaces and parentheses, e.g.

ERR15660424_SequelII_PRJEB97182.fastq.gz

allowed the rerun to progress past the previous syntax error and reach running state.

Suggested fix

Quote the generated input filename in the sylph sketch command, or avoid dataset-derived filenames in shell commands entirely by using a fixed safe symlink name such as input.fastq.gz.