Add the two current workflows to this fork

[fubar2]

Just lost a few days work trying to push this - my git-fu is too weak and it will be much safer for me if we work in a real repository :(

[fubar2]

Git diffs of .ga files are really not helpful. Did not edit anything - just added the two new WF.
Might be easier for you to download and push these yourself rather than merge this PR?
From that update:
TreeValGalAugTwoHaps:
Current WF on VGP

Dimers, coverage, SV:
Current WF on VGP

[fubar2]

managed to recover the draft IWC tests.
The dimer workflow now passes tests with some very small fastq/fasta so git does not grizzle about file sizes.

Will get the main one working too, then make a PR for the main IWC repository.
Far prefer to try to work on the main IWC repository in future - I am hopeless with git and get bamboozled by trying to push to a fork :(

[Delphine-L]

@fubar2 I made a PR to the IWC to make things easier, galaxyproject#559
Does that work better for you ?

[fubar2]

I made a PR to the IWC to make things easier, galaxyproject#559

@Delphine-L: Thanks!
tl;dr we need to consolidate these as PR for the IWC repository with working tests.

#557 has the two WF I'd like to take forward as EBPhib-describe and EBPhib-dimer-coverage. Both those WF pass planemo tests when run from my machine, but there is a strange error in the CI so the tests don't actually seem to run here on github although they "pass". Sample test files are in https://github.com/fubar2/iwc/tree/EBPhisb/workflows/VGP-assembly-v2/EBPhib-descriptive/test-data and in https://github.com/fubar2/iwc/tree/EBPhisb/workflows/VGP-assembly-v2/EBPhib-dimer-coverage-SV/test-data

The pretext WF is one I don't know anything about. It seems to be generating stand-alone images rather than tracks to be integrated into JBrowse2, and needs test data starting with matching subsamples of HiC F/R reads, to map against subsampled haplotype fasta. Fake telomere/gap bed features are easy to make up, and the small HiC reads and the small haplotypes can be mapped and the bam converted to a small coverage bigwig.

Maybe easiest if it becomes an EBPhib subWF because the arima data is the only thing missing