metrics

metrics subworkflow

Quality metrics are at the core of any laboratory process. Donut Falls uses gfastats, nanoplot, busco, and multiqc - although gfastats is included in the assembly subworkflow due to its capacity to detect circular sequences in gfa files. Quast was not included due to its inclusion of Grandeur - which we run our consensus fastas through for further analysis and serotyping.

Nanoplot is run on each fastq file, but can also be run on the summary file created by Nanopore. The summary file can be read into Donut Falls with 'params.sequencing_summary'.

Several tools are still in the process of being developed, so this is the subworkflow that is most likely to add tools in the future. If there is one that would be useful, please submit an issue in this repository.

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Donut Falls
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flowchart LR
C[nanopore fastq files] --> D[nanoplot]
E[nanopore summary file] --> D

A[consensus fastas] --> B[busco]
F[fastp log files] --> G[multiQC]
B --> G

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Relevant parameters (params) and their default values

params.sequencing_summary          = workflow.launchDir + "/*sequencing_summary*txt"
params.busco_options               = ''
params.multiqc_options             = ''
params.nanoplot_summary_options    = ''
params.nanoplot_options            = ''