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snakemake-workflows / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2
MIT License
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SyntaxError in line 14 of Snakefile #45

Closed Blosberg closed 1 year ago

Blosberg commented 2 years ago

Thanks for creating this package. I've followed instructions here through to step 4, at which point when I try to run the workflow I get the following:

$snakemake --cores all -n
SyntaxError in line 14 of /path/to/workflow/Snakefile:
invalid syntax (Snakefile, line 14)

Line 14 being the config: line in the following context

...
module rna_seq_star_deseq2:
    snakefile:
        /path/to/workflow/Snakefile
    config:
        config
...

I can't see anything wrong with my config file. As far as I'm aware the packages from snakemake/deploy are all there. I also undid all of my project-specific entry data to the files in config and set them back to being identical to the original template. Do you have any idea where this is coming from?

dlaehnemann commented 1 year ago

Were you able to solve this? If so, how? If not, maybe there was some other syntax problem in the Snakefile, that only gets thrown in line 14?

I'll close this issue for now, as it has aged quite a bit. But please feel free to reopen, if this persists (or to open another issue, if anything else comes up).