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nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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SyntaxError: Input and output files have to be specified as strings or lists of strings #34

Open correave opened 2 years ago

correave commented 2 years ago

Hello,

I am trying to run the "pipeline-transcriptome-de_phe" that was downloaded from the Github repository (https://github.com/nanoporetech/pipeline-transcriptome-de). I am running this within a Python 3 environment. The config.yml file was modified following the Github example. The pipeline runs briefly until gives me the error message below with no output files.

Error Message

"SyntaxError: Input and output files have to be specified as strings or lists of strings.

File "/work/lab/pipeline-transcriptome-de-2/Snakefile", line 15, in

File "/work/lab/pipeline-transcriptome-de-2/snakelib/utils.snake", line 15, in "

Any suggestions will be appreciated.

EnJun-Yang commented 2 years ago

Maybe a similar issue to #33 ? I've replied to that thread with my workaround, but it's a quick fix, not a proper solution.