Re-assemble if not complete

[hkaspersen]

For the hybrid assembly track, the goal is to generate a complete assembly where all the contigs have the tag circular=true (given that this is biologically true). However, this is not always so easy, and it might require an extra run with stricter settings with unicycler if not managed the first round. Thus, it would be beneficial to consider adding in a step that will re-run the filtlong/hybrid assembly step if the criteria are not met.
This may be implemented like this:

Initial filtering and assembly using "default" pipeline settings that fits most cases
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Check if all contigs have the circular=true flag
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if all contigs are marked, then complete pipeline for this isolate and output results
If not, run assembly step again with --mode=bold.
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if all contigs are marked, then complete pipeline for this isolate and output results
if not, run stricter filtering with filtlong and assembly step again with mode=bold
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output results regardless of outcome, and report on all genomes

[hkaspersen]

This may be changed in the future, as the short-read-first method may be redundant. Due to the increasing quality and depth of nanopore sequencing, long-read-first assembly is becoming more and more popular. Therefore it might be prudent in the future to add Circlator as a separate step in a long-read assembly track