mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 20:19:55 +00:00
341 lines
9.1 KiB
YAML
341 lines
9.1 KiB
YAML
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"
|
|
- "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: "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."
|
|
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: "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."
|
|
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:
|
|
"% Unclassified": False
|
|
"% Top 5": False
|
|
Bracken:
|
|
"% Unclassified": False
|
|
"% Top 5": False
|
|
Centrifuge: False
|
|
DIAMOND:
|
|
queries_aligned: False
|
|
Kaiju:
|
|
assigned: False
|
|
"% Assigned": False
|
|
"% Unclassified": False
|
|
MALT:
|
|
"Num. of queries": False
|
|
Total reads: False
|
|
Mappability: False
|
|
Assig. Taxonomy: False
|
|
Taxonomic assignment success: False
|
|
motus:
|
|
Total number of reads: False
|
|
Number of reads after filtering: False
|
|
Total number of inserts: False
|
|
Unique mappers: False
|
|
Multiple mappers: False
|
|
Ignored multiple mapper without unique hit: False
|
|
"Number of ref-mOTUs": False
|
|
"Number of meta-mOTUs": False
|
|
"Number of ext-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."
|