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 - bbduk - prinseqplusplus - porechop - filtlong - bowtie2 - minimap2 - samtools - kraken - kaiju - metaphlan - diamond - malt - motus - custom_content sp: diamond: contents: "diamond v" num_lines: 10 fastqc/data: fn_re: ".*[fastqc|falco]_data.txt" fastqc/zip: fn: "*_fastqc.zip" #extra_fn_clean_exts: # - '_fastp' # - '.pe.settings' # - '.se.settings' top_modules: - "fastqc": name: "FastQC / Falco (pre-Trimming)" path_filters: - "*raw*" path_filters_exclude: - "*processed*" extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." - "fastqc": name: "FastQC / Falco (post-Trimming)" path_filters: - "*processed*" path_filters_exclude: - "*raw*" extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." - "fastp" - "adapterRemoval" - "porechop": extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated." - "bbduk" - "prinseqplusplus" - "filtlong" - "bowtie2": name: "bowtie2" - "samtools": name: "Samtools Stats" - "kraken": name: "Kraken" path_filters: - "*.kraken2.kraken2.report.txt" - "kraken": name: "Bracken" anchor: "bracken" target: "Bracken" doi: "10.7717/peerj-cs.104" info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree." extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC." path_filters: - "*.bracken.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: "ℹ️: 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" - "malt": name: "MALT" - "diamond" - "kaiju": name: "Kaiju" - "motus" #It is not possible to set placement for custom kraken and centrifuge columns. table_columns_placement: FastQC / Falco (pre-Trimming): total_sequences: 100 avg_sequence_length: 110 median_sequence_length: 120 percent_duplicates: 130 percent_gc: 140 percent_fails: 150 FastQC / Falco (post-Trimming): total_sequences: 200 avg_sequence_length: 210 median_sequence_length: 220 percent_duplicates: 230 percent_gc: 240 percent_fails: 250 fastp: pct_adapter: 300 pct_surviving: 310 pct_duplication: 320 after_filtering_gc_content: 330 after_filtering_q30_rate: 340 after_filtering_q30_bases: 350 filtering_result_passed_filter_reads: 360 Adapter Removal: aligned_total: 360 percent_aligned: 370 percent_collapsed: 380 percent_discarded: 390 Porechop: Input Reads: 400 Start Trimmed: 410 Start Trimmed Percent: 420 End Trimmed: 430 End Trimmed Percent: 440 Middle Split: 450 Middle Split Percent: 460 Filtlong: Target bases: 500 BBDuk: Input reads: 800 Total Removed bases percent: 810 Total Removed bases: 820 Total Removed reads percent: 830 Total Removed reads: 840 PRINSEQ++: prinseqplusplus_total: 900 bowtie2: overall_alignment_rate: 1000 Samtools Stats: raw_total_sequences: 1100 reads_mapped: 1110 reads_mapped_percent: 1120 reads_properly_paired_percent: 1130 non-primary_alignments: 1140 reads_MQ0_percent: 1150 error_rate: 1160 Bracken: "% Unclassified": 1200 "% Top 5": 1210 Centrifuge: "% Unclassified": 1300 "% Top 5": 1310 DIAMOND: queries_aligned: 1400 Kaiju: assigned: 1500 "% Assigned": 1510 "% Unclassified": 1520 Kraken: "% Unclassified": 1600 "% Top 5": 1610 MALT: "Num. of queries": 1700 Total reads: 1710 Mappability: 1720 Assig. Taxonomy: 1730 Taxonomic assignment success: 1740 motus: Total number of reads: 1800 Number of reads after filtering: 1810 Total number of inserts: 1820 Unique mappers: 1830 Multiple mappers: 1840 Ignored multiple mapper without unique hit: 1850 "Number of ref-mOTUs": 1860 "Number of meta-mOTUs": 1870 "Number of ext-mOTUs": 1880 table_columns_visible: FastQC / Falco (pre-Trimming): total_sequences: True avg_sequence_length: True percent_duplicates: True percent_gc: True percent_fails: False FastQC / Falco (post-Trimming): total_sequences: True avg_sequence_length: True percent_duplicates: False percent_gc: False percent_fails: False porechop: Input reads: False Start Trimmed: Start Trimmed Percent: True End Trimmed: False End Trimmed Percent: True Middle Split: False Middle Split Percent: True fastp: pct_adapter: True pct_surviving: True pct_duplication: False after_filtering_gc_content: False after_filtering_q30_rate: False after_filtering_q30_bases: False Filtlong: Target bases: True Adapter Removal: aligned_total: True percent_aligned: True percent_collapsed: True percent_discarded: False BBDuk: Input reads: False Total Removed bases Percent: False Total Removed bases: False Total Removed reads percent: True Total Removed reads: False "PRINSEQ++": prinseqplusplus_total: True bowtie2: overall_alignment_rate: True Samtools Stats: raw_total_sequences: True reads_mapped: True reads_mapped_percent: True reads_properly_paired_percent: False non-primary_alignments: False reads_MQ0_percent: False error_rate: False Kraken: False Bracken: False Centrifuge: False DIAMOND: False Kaiju: False MALT: False motus: False table_columns_name: FastQC / Falco (pre-Trimming): total_sequences: "Nr. Input Reads" avg_sequence_length: "Length Input Reads" percent_gc: "% GC Input Reads" percent_duplicates: "% Dups Input Reads" percent_fails: "% Failed Input Reads" FastQC / Falco (post-Trimming): total_sequences: "Nr. Processed Reads" avg_sequence_length: "Length Processed Reads" percent_gc: "% GC Processed Reads" percent_duplicates: "% Dups Processed Reads" percent_fails: "% Failed Processed Reads" Samtools Stats: raw_total_sequences: "Nr. Reads Into Mapping" reads_mapped: "Nr. Mapped Reads" reads_mapped_percent: "% Mapped Reads" extra_fn_clean_exts: - "kraken2.report.txt" - ".txt" - ".settings" - ".bbduk" - ".unmapped" - "_filtered" - type: remove pattern: "_falco" section_comments: general_stats: "By default, all read count columns are displayed as millions (M) of reads."