ChromHMM enhancer extension

[LeonHafner]

This pull request introduces the Enhancer Prediction with ChromHMM, as described in Issue #63.
The changes have not yet been tested and are not yet complete.

TODO:

• Add better way to create the cellmarkfiletable using the input csv for ehmm
• Add java container for BINARIZE_BAMS and LEARN_MODEL processes
• Get parameters from the config file (organism, genome version, ...)
• Add nf-core meta object to the input and output channels of the processes

[github-actions]

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[nictru]

Copy-pasting files from another repo is not a good practice, we should do one of the following:

• Reference files from there as Permalinks to the original repo directly in the igenomes config (preferable)
• Add the repo as git submodule

Resulting TODO list:

• Remove chromHMM files from this Repo
• Add meta entries to all processes, will contain metadata from the design file (state, assay) as well as a unique id (which should be added as tag to each process)
• Add labels to each process (important for resource allocation)
• Add java docker images: Even if it runs on our cluster, it does not have to run on every user's system
• I thought of something else and forgot it, will at later if it comes to my mind again

[LeonHafner]

I integrated the ChromHMM workflow into the main pipeline and testet it.
This part should be done from my side and can be merged.
Feel free to make any necessary corrections before approving the merge.

[nictru]

Implementation looks fine, but the ChromHMM output is not yet used in any way - should clarify in today's meeting how to proceed with EHMM and than make the necessary connections

[LeonHafner]

I integrated the output of ChromHMM/Rose into the pipeline. This should finish the work on ChromHMM/Rose. Feel free to merge the PR or request further changes if needed.