millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-10 23:23:09 +00:00
Code Issues Releases Packages Activity
taxprofiler/assets/multiqc_config.yml
James Fellows Yates 01fca90496 Tweak MultiQC config [skip ci]
2023-01-31 11:08:46 +01:00

320 lines
8.7 KiB
YAML
Raw Blame History

This file contains invisible Unicode characters

This file contains invisible Unicode characters that are indistinguishable to humans but may be processed differently by a computer. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

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:
contents: "diamond v"
num_lines: 10
#extra_fn_clean_exts:
# - '_fastp'
# - '.pe.settings'
# - '.se.settings'
top_modules:
- "fastqc":
name: "FastQC (pre-Trimming)"
path_filters:
- "*raw_*fastqc.zip"
- "fastqc":
name: "Falco (pre-Trimming)"
path_filters:
- "*_raw_falco_*_report.html"
- "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."
- "fastqc":
name: "FastQC (post-Trimming)"
path_filters:
- "*_processed_*fastqc.zip"
- "fastqc":
name: "Falco (post-Trimming)"
path_filters:
- "*_processed_falco_*_report.html"
- "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 (pre-Trimming):
total_sequences: 100
avg_sequence_length: 110
median_sequence_length: 120
percent_duplicates: 130
percent_gc: 140
percent_fails: 150
Falco (pre-Trimming):
total_sequences: 200
avg_sequence_length: 210
percent_duplicates: 220
percent_gc: 230
percent_fails: 240
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
FastQC (post-Trimming):
total_sequences: 600
avg_sequence_length: 610
median_sequence_length: 620
percent_duplicates: 630
percent_gc: 640
percent_fails: 650
Falco (post-Trimming):
total_sequences: 700
avg_sequence_length: 710
percent_duplicates: 720
percent_gc: 730
percent_fails: 740
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 (pre-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_fails: False
Falco (pre-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_fails: False
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
porechop:
Input reads: False
Start Trimmed:
Start Trimmed Percent: True
End Trimmed: False
End Trimmed Percent: True
Middle Split: False
Middle Split Percent: True
Filtlong:
Target bases: True
Adapter Removal:
aligned_total: True
percent_aligned: True
percent_collapsed: True
percent_discarded: False
FastQC (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
Falco (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: 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 (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"
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 (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"
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"
- "_processed"
section_comments:
general_stats: "By default, all read count columns are displayed as millions (M) of reads."
Reference in a new issue View git blame Copy permalink