mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-12-04 19:29:56 +00:00
281 lines
7.9 KiB
YAML
281 lines
7.9 KiB
YAML
report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/taxprofiler" target="_blank">nf-core/taxprofiler</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/taxprofiler" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-taxprofiler-methods-description":
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order: -1000
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software_versions:
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order: -1001
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"nf-core-taxprofiler-summary":
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order: -1002
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export_plots: true
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custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
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custom_logo_url: https://nf-co.re/taxprofiler
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custom_logo_title: "nf-core/taxprofiler"
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run_modules:
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- fastqc
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- adapterRemoval
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- fastp
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- bbduk
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- prinseqplusplus
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- porechop
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- filtlong
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- bowtie2
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- minimap2
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- samtools
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- kraken
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- kaiju
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- metaphlan
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- diamond
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- malt
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- motus
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- custom_content
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sp:
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diamond:
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fn_re: ".*.diamond.log$"
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fastqc/data:
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fn_re: ".*(fastqc|falco)_data.txt$"
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fastqc/zip:
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fn: "*_fastqc.zip"
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top_modules:
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- "fastqc":
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name: "FastQC / Falco (pre-Trimming)"
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path_filters:
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- "*raw*"
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path_filters_exclude:
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- "*processed*"
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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."
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- "fastqc":
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name: "FastQC / Falco (post-Trimming)"
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path_filters:
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- "*processed*"
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path_filters_exclude:
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- "*raw*"
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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."
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- "fastp"
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- "adapterRemoval"
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- "porechop":
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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."
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- "bbduk"
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- "prinseqplusplus"
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- "filtlong"
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- "bowtie2":
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name: "bowtie2"
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- "samtools":
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name: "Samtools Stats"
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- "kraken":
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name: "Kraken"
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path_filters:
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- "*.kraken2.kraken2.report.txt"
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- "kraken":
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name: "Bracken"
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anchor: "bracken"
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target: "Bracken"
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doi: "10.7717/peerj-cs.104"
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info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
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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."
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path_filters:
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- "*.bracken.kraken2.report.txt"
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- "kraken":
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name: "Centrifuge"
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anchor: "centrifuge"
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target: "Centrifuge"
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doi: "10.1101/gr.210641.116"
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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"
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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."
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path_filters:
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- "*.centrifuge.txt"
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- "malt":
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name: "MALT"
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- "diamond"
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- "kaiju":
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name: "Kaiju"
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- "motus"
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#It is not possible to set placement for custom kraken and centrifuge columns.
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table_columns_placement:
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FastQC / Falco (pre-Trimming):
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total_sequences: 100
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avg_sequence_length: 110
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median_sequence_length: 120
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percent_duplicates: 130
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percent_gc: 140
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percent_fails: 150
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FastQC / Falco (post-Trimming):
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total_sequences: 200
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avg_sequence_length: 210
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median_sequence_length: 220
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percent_duplicates: 230
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percent_gc: 240
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percent_fails: 250
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fastp:
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pct_adapter: 300
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pct_surviving: 310
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pct_duplication: 320
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after_filtering_gc_content: 330
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after_filtering_q30_rate: 340
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after_filtering_q30_bases: 350
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filtering_result_passed_filter_reads: 360
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Adapter Removal:
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aligned_total: 360
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percent_aligned: 370
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percent_collapsed: 380
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percent_discarded: 390
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Porechop:
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Input Reads: 400
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Start Trimmed: 410
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Start Trimmed Percent: 420
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End Trimmed: 430
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End Trimmed Percent: 440
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Middle Split: 450
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Middle Split Percent: 460
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Filtlong:
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Target bases: 500
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BBDuk:
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Input reads: 800
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Total Removed bases percent: 810
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Total Removed bases: 820
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Total Removed reads percent: 830
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Total Removed reads: 840
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PRINSEQ++:
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prinseqplusplus_total: 900
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bowtie2:
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overall_alignment_rate: 1000
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Samtools Stats:
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raw_total_sequences: 1100
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reads_mapped: 1110
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reads_mapped_percent: 1120
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reads_properly_paired_percent: 1130
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non-primary_alignments: 1140
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reads_MQ0_percent: 1150
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error_rate: 1160
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Bracken:
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"% Unclassified": 1200
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"% Top 5": 1210
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Centrifuge:
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"% Unclassified": 1300
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"% Top 5": 1310
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DIAMOND:
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queries_aligned: 1400
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Kaiju:
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assigned: 1500
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"% Assigned": 1510
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"% Unclassified": 1520
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Kraken:
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"% Unclassified": 1600
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"% Top 5": 1610
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MALT:
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"Num. of queries": 1700
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Total reads: 1710
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Mappability: 1720
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Assig. Taxonomy: 1730
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Taxonomic assignment success: 1740
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motus:
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Total number of reads: 1800
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Number of reads after filtering: 1810
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Total number of inserts: 1820
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Unique mappers: 1830
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Multiple mappers: 1840
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Ignored multiple mapper without unique hit: 1850
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"Number of ref-mOTUs": 1860
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"Number of meta-mOTUs": 1870
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"Number of ext-mOTUs": 1880
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table_columns_visible:
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FastQC / Falco (pre-Trimming):
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total_sequences: True
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avg_sequence_length: True
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percent_duplicates: True
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percent_gc: True
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percent_fails: False
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FastQC / Falco (post-Trimming):
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total_sequences: True
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avg_sequence_length: True
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percent_duplicates: False
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percent_gc: False
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percent_fails: False
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porechop:
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Input reads: False
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Start Trimmed:
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Start Trimmed Percent: True
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End Trimmed: False
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End Trimmed Percent: True
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Middle Split: False
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Middle Split Percent: True
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fastp:
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pct_adapter: True
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pct_surviving: True
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pct_duplication: False
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after_filtering_gc_content: False
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after_filtering_q30_rate: False
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after_filtering_q30_bases: False
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Filtlong:
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Target bases: True
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Adapter Removal:
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aligned_total: True
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percent_aligned: True
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percent_collapsed: True
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percent_discarded: False
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BBDuk:
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Input reads: False
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Total Removed bases Percent: False
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Total Removed bases: False
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Total Removed reads percent: True
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Total Removed reads: False
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"PRINSEQ++":
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prinseqplusplus_total: True
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bowtie2:
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overall_alignment_rate: True
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Samtools Stats:
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raw_total_sequences: True
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reads_mapped: True
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reads_mapped_percent: True
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reads_properly_paired_percent: False
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non-primary_alignments: False
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reads_MQ0_percent: False
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error_rate: False
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Kraken: False
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Bracken: False
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Centrifuge: False
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DIAMOND: False
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Kaiju: False
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MALT: False
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motus: False
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table_columns_name:
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FastQC / Falco (pre-Trimming):
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total_sequences: "Nr. Input Reads"
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avg_sequence_length: "Length Input Reads"
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percent_gc: "% GC Input Reads"
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percent_duplicates: "% Dups Input Reads"
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percent_fails: "% Failed Input Reads"
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FastQC / Falco (post-Trimming):
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total_sequences: "Nr. Processed Reads"
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avg_sequence_length: "Length Processed Reads"
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percent_gc: "% GC Processed Reads"
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percent_duplicates: "% Dups Processed Reads"
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percent_fails: "% Failed Processed Reads"
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Samtools Stats:
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raw_total_sequences: "Nr. Reads Into Mapping"
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reads_mapped: "Nr. Mapped Reads"
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reads_mapped_percent: "% Mapped Reads"
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extra_fn_clean_exts:
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- "kraken2.report.txt"
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- ".txt"
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- ".settings"
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- ".bbduk"
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- ".unmapped"
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- "_filtered"
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- type: remove
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pattern: "_falco"
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section_comments:
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general_stats: "By default, all read count columns are displayed as millions (M) of reads."
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