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Add list of expected tools in MultiQC report [skip ci]

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James Fellows Yates 2023-01-31 13:09:53 +01:00
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docs/output.md
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@ -427,6 +427,27 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
All tools in taxprofiler supported by MultiQC will have a dedicated section showing summary statistics of each tool based on information stored in log files. All tools in taxprofiler supported by MultiQC will have a dedicated section showing summary statistics of each tool based on information stored in log files.
You can expect in the MultiQC reports either sections and/or general stats columns for the following tools:
- fastqc
- adapterRemoval
- fastp
- bbduk
- prinseqplusplus
- porechop
- filtlong
- bowtie2
- minimap2
- samtools (stats)
- kraken
- bracken
- centrifuge
- kaiju
- metaphlan
- diamond
- malt
- motus
> ℹ️ The 'General Stats' table by default will only show statistics referring to pre-processing steps, and will not display possible values from each classifier/profiler, unless turned on by the user within the 'Configure Columns' menu or via a custom MultiQC config file (`--multiqc_config`) > ℹ️ The 'General Stats' table by default will only show statistics referring to pre-processing steps, and will not display possible values from each classifier/profiler, unless turned on by the user within the 'Configure Columns' menu or via a custom MultiQC config file (`--multiqc_config`)
### Pipeline information ### Pipeline information