New bulk 5'-RACE supported protocol, non-overlaping reads rescue

[JustBioinfo]

This PR adds :

• a new supported library_generation_method to allow the analysis of 5'RACE library where R1 reads not start directly by the UMI by adding a new process PRESTO_MASKPRIMERS_ALIGN_TRIM that launch MaskPrimers.py align in trim mode before PRESTO_MASKPRIMERS_UMI process.
• an option --assemblepairs_join to allow non-overlapping reads to be rescued using assemblepairs join on failed reads from assemblepairs align. In fact, in our libraries we have a large proportion of reads which do not overlap, but which turn out to be detected as productive sequences at the end of the pipeline.

This PR doesn't add it at the moment but is it possible to have in options the possibility of opting for IgBlast's 19-column mode ?

enhancement #342

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/airrflow branch on the nf-core/test-datasets repository.

Do I need to add tests, and if so, can you tell me how?
So far I've been testing with real data sets from my research lab, should I add a test data set on nf-core/airrflow branch on the nf-core/test-datasets repository ? If so, I'll check with my team to see what I can provide.

• Make sure your code lints (nf-core lint).

LookupError: Failed to clone from the remote: https://github.com/nf-core/modules.git``

• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.

I'm new to analyzing this type of data, so I'm not familiar with the various AIRR library generation methods. Can you help me to name the new supported protocols, so far I've called it specific_5p_race_umi but I'm not sure it's the right way to name it.

• Output Documentation in docs/output.md is updated.
  Have two new output folders, :

  • presto/trim_upstream_umi_linker to store R1 reads where the UMI upstream sequence was trim.
  • presto/08-assemble-pairs-join if the new --assemblepairs_join option is enabled.
    Are they well named to update docs/output.md ?

• CHANGELOG.md is updated.

[JustBioinfo]

Hi,

why remove specific_5p_race_umi from nextflow_schema.json ?
I can't find any comments on my pull request, what should I do next please ?
Thank you very much.