Enhancement snakemake analysis #472
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… THIS NAME CHANGE
…ables more manageable
mmeds/database/database.py
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| @@ -1036,7 +1036,6 @@ def get_sequencing_run_locations(self, metadata, user, column=("RawDataProtocol" | |||
| for run in df[column]: | |||
| if run not in runs: | |||
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this conditional confuses me
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you're right this is bad, it's an old bit of code from before I knew about the unique() function, fixed it now.
mmeds/snakemake/rules/common.smk
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Is this the file that parallelization fails?
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no, this file just has the functions that define what splits will be requested when snakemake is called. nothing actually running from this when those errors occur
| iterations: 5 | ||
| permutations: 5 | ||
| type: spearman | ||
| alpha_metrics: all |
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where do the parameters for sparCC go?
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those SparCC parameters are example parameters from earlier MMEDS where you would specify additional analysis in this config file. Basically it was trying to say "after running standard analysis, also run SparCC". So that's no longer a valid example. But in terms of what about running SparCC otherwise, haven't gotten to that yet, will be part of a future PR
Pull Request Template for MMEDS
What has changed
This PR will move MMEDS analysis from a structure using "Tool" classes -- individual files for each process with decentralized ability to be modified -- to a central Analysis class that makes use of snakemake workflows. The two workflows included in this release are a 'core_pipeline_taxonomic', replacing and improving on the old "Qiime2" tool, and 'lefse', a vast improvement over the old lefse tool.
Checklist of pre-requisites
How to use the feature
Analyses are started in the same ways they were previously: running the script run_analysis.py, or navigating to the Analysis page of the website and putting the information in there. There are new config templates, those can be found in
resourcesunderconfig_file.yamlandlefse_config.yaml.Additional notes
I've decided to deprecate summaries for now. They're odd at best and usually completely useless in their current form. Leaving the summary file in entirely commented to allow for future reference or support.
Issue Closings
Closes #466
Closes #457 (will move the relevant comments to a new issue)
Closes #449
Closes #386
Closes #400
Closes #430
Closes #438
Closes #437
Closes #382