Conflicting Inputs: run_bracken in Config File and Bracken Report Listed in sample_reports

[Battamama]

Hello, I’ve been trying to run the kraken2_classification pipeline using my own Kraken reports, but I keep encountering the following error:

Conflicting` inputs: run_bracken in config file and bracken report listed in sample_reports

Setup:

Cloned git repo
Environment: Using Conda environment with Snakemake and Singularity
Database: Kraken2 database stored locally at /home/nuphys/data/sMETASeq/kraken2_DB
Command used to run the pipeline:

snakemake -s kraken2_classification/Snakefile_downstream_only --configfile config.yaml --use-singularity -j32

Steps Taken:
1- I’m working exclusively with Kraken reports and don’t have Bracken reports, so I’ve set run_bracken: false in the config.yaml.
2- The sample_reports.tsv contains only two columns for sample names and Kraken reports, with no third column for Bracken reports:

    # sample_name  kraken_report
Saliva-Ctr1  /home/nuphys/data/sMETASeq/KrakenReports/Saliva-Ctr1_1.kraken_report.csv
Saliva-Ctr2  /home/nuphys/data/sMETASeq/KrakenReports/Saliva-Ctr2_1.kraken_report.csv

3- I’ve verified that there are no trailing tabs or additional columns in the sample_reports.tsv file.
4- I’ve tried setting run_bracken: true and rerunning the pipeline, but I still receive the same error.
5- I’ve attempted commenting out or removing Bracken-related rules from the Snakefile_downstream_only.
6- I also ensured that the config.yaml file contains no other references to Bracken beyond run_bracken: false.

No matter what I try, the pipeline still gives the same error.

Is there a specific place in the pipeline where the logic enforces the presence of Bracken reports even when run_bracken is set to false? Am I missing any configuration steps to properly bypass Bracken processing?

Any help or insights would be greatly appreciated!