hotfix for _entry.id

[gbouras13]

Just leaving this here in case you find it useful.

Yesterday, Maxim, Rachel and I realised that the current documentation & setup & nextflow pipeline was leaving us with _entry.id that includes -model-${params.version} e.g. -model-v1 for my ATBC data. However, it is desired that the _entry.id does not include this.

After some digging, we realised that _entry.id is created based on the input .pdb filename - so our options were:

1. rename the input .pdb file to ${entry}.pdb omitting -model-${params.version} ; or
2. modify the .cif file afterwards with some kind of custom script.

This nextflow script is updated to implement option 1.

I also note here that you also need to make sure the first .cif made by runModelCifGenerator does not include -model-${params.version}, or else DSSP will not add the right tag either and the resulting mmcif fails gemmi validation.

So the input to DSSP needs to also be ${entry}.cif. Only after DSSP is run can the output include -model-${params.version} . This is implemented in this PR.

I note that this code works, but it includes in its output the intermediate${entry}.cif (which does not include the DSSP information). I am a nextflow rookie and don't have time to spare, so I am not going to invest time into figuring out how to delete these intermediate mmcifs in the pipeline (I am just doing it manually after the pipeline is run at this point), but I am sure you can figure it out.

George