search

NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
19 stars 15 forks source link

How to run only krakenuniq part of the pipeline? (A specific option in the config file is needed) #140

Open emrahkirdok opened 7 months ago

emrahkirdok commented 7 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 7 months ago

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