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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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write_samples.py producing a Type Error #96

Closed ediamant closed 1 year ago

ediamant commented 1 year ago

Hello,

Thank you for putting together this workflow! I am new to bioinformatics, and grateful for this resource. I am trying to run it on ~60 samples of Dark-eyed Junco sequences with a reference genome using an accession number. I've managed to configure things to run on one sample, but am trying to make a sample sheet through the automated code provided for the remaining samples. When I run it, I receive the following error: TypeError: write_sample_sheet() missing 1 required positional argument: 'ncbi_ref' I'm sharing my code below. Any help is appreciated! Thank you!

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tsackton commented 1 year ago

I pushed a change to the 'bugfix' branch that I believe should fix this error. Can you test and let me know if you are still getting problems?

From your local snpArcher repo you'll need to checkout the bugfix branch and then pull the latest changes.

ediamant commented 1 year ago

Thank you! Yes, that fixes the Type Error. However, now it's writing/requesting a path for the files relative to the workflow folder instead of the snpArcher folder. Is there a way to fix that?

tsackton commented 1 year ago

I think it will be simpler if you specify an absolute path in the -f option instead of a relative path. That should fix any path related errors you are getting.