Snakemake showing error with "rna" tag in the sample.yaml

[yashcrux]

Hi,

I am trying to run the snakemake command. an error is popping up to provide "starReferencePath"
snakemake -c 1 --use-singularity --singularity-args "-B /mnt/c/Users/yashd/Desktop/IMPALA" /mnt/c/Users/yashd/Desktop/IMPALA/Snakefile:421: SyntaxWarning: invalid escape sequence '\|' rule figures: /mnt/c/Users/yashd/Desktop/IMPALA/Snakefile:431: SyntaxWarning: invalid escape sequence '\|' log: "output/{sample}/log/figures.log" KeyError in file "/mnt/c/Users/yashd/Desktop/IMPALA/Snakefile", line 96: 'starReferencePath' File "/mnt/c/Users/yashd/Desktop/IMPALA/Snakefile", line 96, in <module>

Even though ots not required, as stated in the documentation, when we are providing with the RNA bam files.

Thanks

[oneillkza]

Looks likely to be issues with newer Python versions: snakemake/snakemake#3232 (comment)

You could try an older Python, or the fix outlined there.

[yashcrux]

Also If I would like to use R1 and R2 instead of rna bam then do I need to have STAR and RSEM preconfigured with their paths known.
The documentation does not state this explicitely!

[oneillkza]

All of the steps specify a Docker container. If you're not running the workflow with a container engine (Docker, Singularity, Apptainer, etc), then yes, you'd need to have all of the tools on the path when the workflow runs.

It would be much, much easier to run this workflow using a container engine.