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Arcadia-Science / metagenomics

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
MIT License
34 stars 2 forks source link

Eam/multiqc #37

Closed elizabethmcd closed 1 year ago

elizabethmcd commented 1 year ago

This PR adds MultiQC reporting support for both the Illumina and Nanopore workflows. Depending on which --platform parameter is run, this corresponds with different Illumina and Nanopore multiqc reports (which are attached as PDFs). For these reports there are a couple of QC modules added such as Nanoplot for Nanopore reads, and QUAST for assessing assemblies. I haven't finished the methods description for these yet because there are more modules to add so I will do that last.

There are also some fixes to the mapping_depth subworkflows and corresponding modules in here that I found while putting this together. Some of it is making fixes to things back from when I didn't quite know what I was doing with the Illumina mapping modules and making input/output handling a little simpler.

Also my Github CI tests aren't coming up and I don't know why...possibly meaning there is something wrong where I merged #33

multiqc_report_nanopore.pdf multiqc_report_short.pdf

elizabethmcd commented 1 year ago

Update: accidentally didn't have all the CI in the dedicated workflows directory in .github and is now fixed and running tests

elizabethmcd commented 1 year ago

SUCCESS