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taxprofiler/assets/multiqc_config.yml
James Fellows Yates 1eb951715f MultiQC optimisations for DIAMOND and Falco
2023-04-20 15:57:57 +02:00

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report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/taxprofiler" target="_blank">nf-core/taxprofiler</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/taxprofiler" target="_blank">documentation</a>.
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:
fn_re: ".*.diamond.log$"
fastqc/data:
fn_re: ".*(fastqc|falco)_data.txt$"
fastqc/zip:
fn: "*_fastqc.zip"
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."
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