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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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Whitespaces in config/units.tsv #81

Closed aFienemann closed 1 year ago

aFienemann commented 1 year ago

Hello,

i am currently trying to run step 4 of the Workflow: snakemake --cores all --use-conda

Apparently whitespaces are detected in columns fq1 and fq2 in config/units.tsv

Screenshot from 2023-10-13 10-38-59

But there are none in the file, the path is functional. I used LibreOffice to customize the table, but in the Text Editor everything looks fine (Tab-seperated and no additional whitespaces). Am I missing something obvious? Still quite new in the field.

Thanks a lot!

tedil commented 1 year ago

Are you by any chance using python 3.12? If so, it might be this issue: https://github.com/snakemake/snakemake/issues/2480

aFienemann commented 1 year ago

That was indeed the case. Thanks a lot!

dlaehnemann commented 1 year ago

Then, I hope that something like the following fix solves this for you: https://github.com/snakemake/snakemake/issues/2480#issuecomment-1765902814

So I'll close this issue, but feel free to reopen or open new issues with other problems.