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multiqc_config_illumina.yml
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report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/viralrecon" target="_blank">nf-core/viralrecon</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://github.com/nf-core/viralrecon" target="_blank">documentation</a>.
data_format: "yaml"
max_table_rows: 10000
run_modules:
- custom_content
- fastqc
- fastp
- kraken
- bowtie2
- samtools
- mosdepth
- bcftools
- snpeff
- quast
- pangolin
- cutadapt
module_order:
- fastqc:
name: "PREPROCESS: FastQC (raw reads)"
info: "This section of the report shows FastQC results for the raw reads before adapter trimming."
path_filters:
- "*/fastqc/*.zip"
- fastp:
name: "PREPROCESS: fastp (adapter trimming)"
info: "This section of the report shows fastp results for reads after adapter and quality trimming."
- kraken:
name: "PREPROCESS: Kraken 2"
info: "This section of the report shows Kraken 2 classification results for reads after adapter trimming with fastp."
- bowtie2:
name: "VARIANTS: Bowtie 2"
info: "This section of the report shows Bowtie 2 mapping results for reads after adapter trimming and quality trimming."
- samtools:
name: "VARIANTS: SAMTools (raw)"
anchor: "samtools_bowtie2"
info: "This section of the report shows SAMTools counts/statistics after mapping with Bowtie 2."
path_filters:
- "*/bowtie2/*"
- samtools:
name: "VARIANTS: SAMTools (iVar)"
anchor: "samtools_ivar"
info: "This section of the report shows SAMTools counts/statistics after primer sequence removal with iVar."
path_filters:
- "*/ivar_trim/*"
- samtools:
name: "VARIANTS: SAMTools (MarkDuplicates)"
anchor: "samtools_markduplicates"
info: "This section of the report shows SAMTools counts/statistics after duplicate removal with picard MarkDuplicates."
path_filters:
- "*/picard_markduplicates/*"
- mosdepth:
name: "VARIANTS: mosdepth"
info: "This section of the report shows genome-wide coverage metrics generated by mosdepth."
- pangolin:
name: "VARIANTS: Pangolin"
info: "This section of the report shows Pangolin lineage analysis results for the called variants."
path_filters:
- "*/variants/*.pangolin.csv"
- bcftools:
name: "VARIANTS: BCFTools"
info: "This section of the report shows BCFTools stats results for the called variants."
path_filters:
- "*/variants/*.txt"
- snpeff:
name: "VARIANTS: SnpEff"
info: "This section of the report shows SnpEff results for the called variants."
path_filters:
- "*/variants/*.csv"
- quast:
name: "VARIANTS: QUAST"
anchor: "quast_variants"
info: "This section of the report shows QUAST QC results for the consensus sequence."
path_filters:
- "*/variants/*.tsv"
- cutadapt:
name: "ASSEMBLY: Cutadapt (primer trimming)"
info: "This section of the report shows Cutadapt results for reads after primer sequence trimming."
- quast:
name: "ASSEMBLY: QUAST (SPAdes)"
anchor: "quast_spades"
info: "This section of the report shows QUAST results from SPAdes de novo assembly."
path_filters:
- "*/assembly_spades/*.tsv"
- quast:
name: "ASSEMBLY: QUAST (Unicycler)"
anchor: "quast_unicycler"
info: "This section of the report shows QUAST results from Unicycler de novo assembly."
path_filters:
- "*/assembly_unicycler/*.tsv"
- quast:
name: "ASSEMBLY: QUAST (minia)"
anchor: "quast_minia"
info: "This section of the report shows QUAST results from minia de novo assembly."
path_filters:
- "*/assembly_minia/*.tsv"
report_section_order:
fail_mapped_reads:
after: summary_variants_metrics
fail_mapped_samples:
after: summary_variants_metrics
summary_assembly_metrics:
before: summary_variants_metrics
amplicon_heatmap:
before: summary_assembly_metrics
ivar_variants:
before: mosdepth
software_versions:
order: -1001
nf-core-viralrecon-summary:
order: -1002
bcftools:
collapse_complementary_changes: true
# See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml
custom_data:
amplicon_heatmap:
section_name: "Amplicon coverage heatmap"
description: "Heatmap to show median log10(coverage+1) per amplicon across samples."
plot_type: "heatmap"
pconfig:
id: "amplicon_heatmap"
xTitle: "Amplicon"
namespace: "Heatmap to show median log10(coverage+1) per amplicon across samples"
square: False
colstops:
[
[0, "#440154"],
[0.05, "#471365"],
[0.1, "#482475"],
[0.15, "#463480"],
[0.2, "#414487"],
[0.25, "#3b528b"],
[0.3, "#355f8d"],
[0.35, "#2f6c8e"],
[0.4, "#2a788e"],
[0.45, "#25848e"],
[0.5, "#21918c"],
[0.55, "#1e9c89"],
[0.6, "#22a884"],
[0.65, "#2fb47c"],
[0.7, "#44bf70"],
[0.75, "#5ec962"],
[0.8, "#7ad151"],
[0.85, "#9bd93c"],
[0.9, "#bddf26"],
[0.95, "#dfe318"],
[1, "#fde725"],
]
summary_variants_metrics:
section_name: "Variant calling metrics"
description: "generated by the nf-core/viralrecon pipeline"
plot_type: "table"
headers:
"# Input reads":
description: "Total number of reads in raw fastq file"
format: "{:,.0f}"
"% Non-host reads (Kraken 2)":
description: "Total number of non-host reads identified by Kraken2"
format: "{:,.2f}"
"# Trimmed reads (fastp)":
description: "Total number of reads remaining after adapter/quality trimming with fastp"
format: "{:,.0f}"
"# Mapped reads":
description: "Total number of Bowtie2 mapped reads relative to the viral genome"
format: "{:,.0f}"
"% Mapped reads":
description: "Percentage of Bowtie2 mapped reads relative to the viral genome"
format: "{:,.2f}"
"# Trimmed reads (iVar)":
description: "Total number of reads remaining after primer trimming with iVar"
format: "{:,.0f}"
"Coverage median":
description: "Median coverage calculated by mosdepth"
format: "{:,.2f}"
"% Coverage > 1x":
description: "Coverage > 1x calculated by mosdepth"
format: "{:,.2f}"
"% Coverage > 10x":
description: "Coverage > 10x calculated by mosdepth"
format: "{:,.2f}"
"# SNPs":
description: "Total number of SNPs"
format: "{:,.0f}"
"# INDELs":
description: "Total number of INDELs"
format: "{:,.0f}"
"# Missense variants":
description: "Total number of variants identified as missense mutations with SnpEff"
format: "{:,.0f}"
"# Ns per 100kb consensus":
description: "Number of N bases per 100kb in consensus sequence"
format: "{:,.2f}"
"Pangolin lineage":
description: "Pangolin lineage inferred from the consensus sequence"
"Nextclade clade":
description: "Nextclade clade inferred from the consensus sequence"
pconfig:
id: "summary_variants_metrics_plot"
table_title: "Variant calling metrics"
namespace: "Variant calling metrics"
only_defined_headers: False
format: "{:.0f}"
summary_assembly_metrics:
section_name: "De novo assembly metrics"
description: "generated by the nf-core/viralrecon pipeline"
plot_type: "table"
headers:
"# Input reads":
description: "Total number of reads in raw fastq file"
format: "{:,.0f}"
"# Trimmed reads (Cutadapt)":
description: "Total number of reads remaining after adapter/quality trimming with fastp"
format: "{:,.0f}"
"% Non-host reads (Kraken 2)":
description: "Total number of non-host reads identified by Kraken2"
format: "{:,.2f}"
"# Contigs (SPAdes)":
description: "Total number of contigs in SPAdes assembly as calculated by QUAST"
format: "{:,.0f}"
"Largest contig (SPAdes)":
description: "Size of largest contig in SPAdes assembly as calculated by QUAST"
format: "{:,.0f}"
"% Genome fraction (SPAdes)":
description: "% genome fraction for SPAdes assembly as calculated by QUAST"
format: "{:,.2f}"
"N50 (SPAdes)":
description: "N50 metric for SPAdes assembly as calculated by QUAST"
format: "{:,.2f}"
"# Contigs (Unicycler)":
description: "Total number of contigs in Unicycler assembly as calculated by QUAST"
format: "{:,.0f}"
"Largest contig (Unicycler)":
description: "Size of largest contig in Unicycler assembly as calculated by QUAST"
format: "{:,.0f}"
"% Genome fraction (Unicycler)":
description: "% genome fraction for Unicycler assembly as calculated by QUAST"
format: "{:,.2f}"
"N50 (Unicycler)":
description: "N50 metric for Unicycler assembly as calculated by QUAST"
format: "{:,.2f}"
"# Contigs (minia)":
description: "Total number of contigs in minia assembly as calculated by QUAST"
format: "{:,.0f}"
"Largest contig (minia)":
description: "Size of largest contig in minia assembly as calculated by QUAST"
format: "{:,.0f}"
"% Genome fraction (minia)":
description: "% genome fraction for minia assembly as calculated by QUAST"
format: "{:,.2f}"
"N50 (minia)":
description: "N50 metric for minia assembly as calculated by QUAST"
format: "{:,.2f}"
pconfig:
id: "summary_assembly_metrics_plot"
table_title: "De novo assembly metrics"
namespace: "De novo assembly metrics"
only_defined_headers: False
format: "{:.0f}"
fail_mapped_reads:
section_name: "WARNING: Fail Reads Check"
description: "List of samples that had no reads after adapter trimming, and hence were ignored for the downstream processing steps."
plot_type: "table"
pconfig:
id: "fail_mapped_reads_table"
table_title: "Samples failed read threshold"
namespace: "Samples failed read threshold"
format: "{:,.0f}"
fail_mapped_samples:
section_name: "WARNING: Fail Alignment Check"
description: "List of samples that failed the Bowtie2 minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."
plot_type: "table"
pconfig:
id: "fail_mapped_samples_table"
table_title: "Samples failed mapped read threshold"
namespace: "Samples failed mapping read threshold"
format: "{:,.0f}"
extra_fn_clean_exts:
- ".markduplicates"
- ".unclassified"
- "_MN908947.3"
- " MN908947.3"
extra_fn_clean_trim:
- "Consensus_"
# # Customise the module search patterns to speed up execution time
# # - Skip module sub-tools that we are not interested in
# # - Replace file-content searching with filename pattern searching
# # - Don't add anything that is the same as the MultiQC default
# # See https://multiqc.info/docs/#optimise-file-search-patterns for details
sp:
fastp:
fn: "*.fastp.json"
bowtie2:
fn: "*.bowtie2.log"
mosdepth/global_dist:
fn: "*.global.dist.txt"
cutadapt:
fn: "*.cutadapt.log"