report_comment: > This report has been generated by the nf-core/taxprofiler analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-taxprofiler-methods-description": order: -1000 software_versions: order: -1001 "nf-core-taxprofiler-summary": order: -1002 export_plots: true custom_logo: "nf-core-taxprofiler_logo_custom_light.png" custom_logo_url: https://nf-co.re/taxprofiler custom_logo_title: "nf-core/taxprofiler" run_modules: - fastqc - adapterRemoval - fastp - bowtie2 - samtools - kraken - malt - custom_content #extra_fn_clean_exts: # - '_fastp' # - '.pe.settings' # - '.se.settings' top_modules: - "fastqc": name: "FastQC (pre-Trimming)" path_filters: - "*raw_*fastqc.zip" - "fastp" - "adapterRemoval" - "fastqc": name: "FastQC (post-Trimming)" path_filters: - "*raw_*processed.zip" - "kraken": name: "Kraken" path_filters: - "*.kraken2.report.txt" - "kraken": name: "Centrifuge" anchor: "centrifuge" target: "Centrifuge" doi: "10.1101/gr.210641.116" info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title" extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above." path_filters: - "*.centrifuge.txt"