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Performs Nanoplot QC using nanoplot and adaptor trimming using downpore

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Capture log output

Need a way to capture the log output of downpore. I had to grab it out of the .command.log file for it but there should be a way to publish that also to the outdir with an appropriate name.

Add system_check process that works with containers.

I don't think the system_check will work with containers. I will have to investigate.

commands log

Is there an easy way to print out all the commands executed by a workflow? This would be useful to see exact parameters used without having to dig through the workflow or git repo.

Add nanoComp process

When there are more than 1 fastq files then run a comparison of the outputs from nanoplot.

nanocomp example

NanoComp --pickle sample01/sample01_NanoPlot-data.pickle sample02/sample02_NanoPlot-data.pickle sample03/sample03_NanoPlot-data.pickle sample04/sample04_NanoPlot-data.pickle sample05/sample05_NanoPlot-data.pickle --names sample01 sample02 sample03 sample04 sample05 -o nanoCompOut -t 36 --title "all samples"

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