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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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How to run only krakenuniq part of the pipeline? (A specific option in the config file is needed) #140

Open emrahkirdok opened 12 months ago

emrahkirdok commented 12 months ago

For a specific project, I only need to run krakenuniq part of the pipeline. Specifically, I want to run Cutadapt_Adapter_Trimming, KrakenUniq, Filter_KrakenUniq_Output, and KrakenUniq_AbundanceMatrix rules.

However the pipeline runs krakenuniq and bowtie2 rules by default. And there is no specific rule to make this distinciton.

So far I managed it by asking snakemake to create results/KRAKENUNIQ_ABUNDANCE_MATRIX/krakenuniq_abundance_matrix.txt file. But it would be very handy if we have an option to run only krakenuniq part.

Thank you

npsonis commented 11 months ago

You can use the --omit-from command of snakemake and exclude the bowtie2 step.