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Gleeson-Lab / wxs_pipeline

Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF
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Implement Downloading/Creating all Reference Data Files #3

Closed brcopeland closed 3 years ago

brcopeland commented 3 years ago

Ideally the pipeline should not have dependencies on data of unknown provenance as is the case when using pre-downloaded files.

brcopeland commented 3 years ago

I implemented this but have observed that snakemake appears to hang indefinitely (or least for a long time) if using remote files. I will set this aside for now.

brcopeland commented 3 years ago

This appears to be the same issue as https://github.com/snakemake/snakemake/issues/373.

brcopeland commented 3 years ago

I am going to close this. As noted this doesn't seem to be a viable option given snakemake limitations. Additionally I've confirmed the integrity of the resource files the pipeline uses and revoked write permissions on these files from everyone else, so we should be fine on this front. The only unfortunate thing is that this is the only aspect of the pipeline that is tied into our environment (would be preferable to have none).