add flagger?

[CeciliaDeng]

Description of feature

Hi @GallVp , @SarahBailey1998 and @ignacio3437 ,

Did you talk about flagger before? In case it is not, the github page said flagger is a HMM- and read alignments-based tool to detect mis-assemblies (erroneous, falsely duplicated, structurally correct, or collapsed) in diploid and haploid assemblies

[GallVp]

Yes, we have talked about it but never got to test it.

Once we have tested it, let's add it to our pipeline.

[SarahBailey1998]

flagger testing scripts are available here: https://github.com/PlantandFoodResearch/bioinf_red_pangenome/blob/7407d66730b4668528133a970df6d6f1b3a60504/version1_assemblies/flagger_test.md