mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-14 07:03:09 +00:00
259 lines
7.1 KiB
YAML
259 lines
7.1 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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- bbduk
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- prinseqplusplus
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- fastp
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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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- porechop
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- custom_content
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#extra_fn_clean_exts:
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# - '_fastp'
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# - '.pe.settings'
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# - '.se.settings'
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top_modules:
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- "fastqc":
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name: "FastQC (pre-Trimming)"
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path_filters:
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- "*raw_*fastqc.zip"
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- "fastqc":
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name: "Falco (pre-Trimming)"
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path_filters:
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- "*_raw_falco_*_report.html"
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- "fastp"
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- "adapterRemoval"
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- "porechop"
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- "fastqc":
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name: "FastQC (post-Trimming)"
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path_filters:
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- "*_processed_*fastqc.zip"
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- "fastqc":
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name: "Falco (post-Trimming)"
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path_filters:
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- "*_processed_falco_*_report.html"
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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: "Note: 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: "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."
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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 (pre-Trimming):
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total_sequences: 100
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avg_sequence_length: 110
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percent_duplicates: 120
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percent_gc: 130
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percent_fails: 140
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Falco (pre-Trimming):
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total_sequences: 200
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avg_sequence_length: 210
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percent_duplicates: 220
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percent_gc: 230
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percent_fails: 240
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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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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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FastQC (post-Trimming):
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total_sequences: 400
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avg_sequence_length: 410
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percent_duplicates: 420
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percent_gc: 430
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percent_fails: 440
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Falco (post-Trimming):
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total_sequences: 500
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avg_sequence_length: 510
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percent_duplicates: 520
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percent_gc: 530
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percent_fails: 540
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bowtie2:
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overall_alignment_rate: 600
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Samtools Stats:
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raw_total_sequences: 700
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reads_mapped: 710
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reads_mapped_percent: 720
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reads_properly_paired_percent: 730
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non-primary_alignments: 740
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reads_MQ0_percent: 750
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error_rate: 760
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MALT:
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Num. of queries: 1000
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Total reads: 1100
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Mappability: 1200
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Assig. Taxonomy: 1300
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Taxonomic assignment success: 1400
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Kaiju:
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assigned: 2000
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"% Assigned": 2100
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"% Unclassified": 2200
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table_columns_visible:
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FastQC (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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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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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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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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FastQC (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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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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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:
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"% Unclassified": True
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"% Top 5": False
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Bracken:
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"% Unclassified": True
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"% Top 5": False
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Centrifuge:
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"% Unclassified": True
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"% Top 5": False
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MALT:
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Num. of queries: True
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Total reads: True
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Mappability: True
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Assig. Taxonomy: False
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Taxonomic assignment success: True
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Kaiju:
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assigned: False
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"% Assigned": False
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"% Unclassified": True
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table_columns_name:
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FastQC (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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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 (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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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.kraken2.report.txt"
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- ".centrifuge.txt"
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- ".bracken.kraken2.report.txt"
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- ".settings"
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