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add: optional import of a vipr snakemake rule #3
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I like the idea. Previously tried doing the same for nextstrain/ncov#921: nextstrain/ncov-tutorial@6125006 But I haven't used Snakemake much to understand - are there any drawbacks to this approach? |
victorlin
reviewed
May 20, 2022
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| module vipr_workflow: | ||
| snakefile: | ||
| github("j23414/test_snakemake_6", path="workflow/vipr.smk", branch="main") |
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Linking here for easy access: https://github.com/j23414/test_snakemake_6/blob/main/workflow/vipr.smk
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| use rule vipr_fasta from vipr_workflow as pull_data with: | ||
| output: | ||
| output="vipr_download.fasta", | ||
| params: | ||
| family='pneumoviridae', | ||
| virus='Respiratory%20syncytial%20virus', |
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Based on ZIKA.md, these are the URL parameters used there:
- datatype=genome
- family=flavi
- species=Zika virus
- fromyear=2013
- minlength=5000
- metadata=genbank,strainname,segment,date,host,country,genotype,species
- output=fasta
Can the rule be generalized to take arbitrary URL parameters, maybe as a single Snakemake param? I notice there's a slight difference between the above and vipr.smk.
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Thanks @victorlin for all the comments! Sorry I never got back to you, my fault. Closing this PR since it may be superseded by a different codebase. |
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Description
This is mainly to start a discussion if we want to use importable snakemake rules to reduce code duplication? The vipr rule is simple enough that it doesn't need to use external python/bash scripts.
Perfectly fine if we want to stick with one Snakefile, just submitting this in case.