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

[emrahkirdok]

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]

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

[LeandroRitter]

@percyfal wasn't it addressed in your old PR #149 which was never merged with the main?

[percyfal]

Alternatively one could have a target that specifically lists the krakenuniq output, e.g.,

rule krakenuniq:
    input:
        all_input["krakenuniq.krona"]

[percyfal]

This target would live in the main Snakefile, after the all rule, and the user would have to run the workflow as snakemake -s workflow/Snakefile ... krakenuniq

[percyfal]

Is setting bowtie=false the same as running only krakenuniq though?

[LeandroRitter]

I think @emrahkirdok meant: "How to make aMeta stop after it generated the KrakenUniq abundance matrix?", i.e. he wanted to skip entirely the rest of the pipeline. I believe disabling bowtie2 does not skip Malt steps. Still it is good to have bowtie=False to be implemented. Ideally, I would say, it would be good to have an option that makes aMeta run QC + AdapterRemoval + KrakenUniq + FilteringKrakenUniq + Krona + KrakenUniqAbundanceMatrix only, and then finishes.

Something like asking snakemake to create results/KRAKENUNIQ_ABUNDANCE_MATRIX/krakenuniq_abundance_matrix.txt file, which @emrahkirdok mentions in his original request

[LeandroRitter]

Or would, what @emrahkirdok was asking above, be equivalent to specifying:

# you can include or exclude certain types of analysis
analyses:
  mapdamage: false
  authentication: false
  malt: false
  krona: true
  bowtie: false

In the config-file? If so, then the PR #149, which you @percyfal developed, should be enough to make aMeta run QC + AdapterRemoval + KrakenUniq + FilteringKrakenUniq + Krona + KrakenUniqAbundanceMatrix only, right?