report

Summary or Final Report

It is helpful to have a small simple file with a summary of information. This file is even better with charts and graphs. As such, three files are generated at the end of the workflow.

1. grandeur_summary.tsv and grandeur_summary.txt
2. grandeur_extended_summary.tsv and grandeur_extended_summary.txt
3. multiqc.html

If you are using nextflow tower to run this workflow (not using -with-tower on the command line), these files should appear in the reports section.

Coverage estimates

Coverage is likely the most important output from this subworkflow, and is dependent on the number of reads, the length of the reads, and the size of the genome in question. There is a json file with the expected sizes of each organism at Grandeur/assets/genome_sizes.json, which is determined by the predicted organism. The end user can supply their own json file with params.genome_sizes. Please submit an issue if a genome size should be adjusted.

Summary

Each process is designed to give some sort of output. These output files are collected and merged into the 'grandeur_extended_summary.tsv' (tab delimited) and 'grandeur_extended_summary.txt' (semi-colon delimited) files in the Grandeur/summary directory. These two files have a lot of columns, so a subset of these columns were chose for '{params.outdir}/grandeur_summary.tsv' (tab delimited) and '{params.outdir}/grandeur_summary.txt' (semi-colon delimited) in the main output directory.

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Summary
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flowchart LR
subworkflows --> extended_summary --> final_summary

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MultiQC

MultiQC is a terrific tool that creates graphs from commonly used tools.

The goal has been to add each analysis to MultiQC is some way - of which some look worse than others.

The MultiQC_report.html file is located in '{params.outdir}/multiqc'.

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MultiQC
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flowchart TD
bbmap --> multiqc
bbduk --> multiqc
kraken2 --> multiqc
fastqc --> multiqc
fastp --> multiqc
quast --> multiqc
prokka --> multiqc
A[custom files] --> mqc_prep
mqc_prep --> multiqc
versions --> multiqc

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Relevant params with their default values:

# used to designate some default values for genomes sizes
params.genome_sizes = "/path/to/genome_sizes.json"