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. 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.
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. 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.multiqc_report_nanopore.pdf multiqc_report_short.pdf