Port pipeline to DSL2

[christopher-mohr]

This

• ports the hlatyping pipeline to DSL2
• uses existing nf-core modules
• merges nf-core template updates until 2.6
• switches to samplesheet input
• adds functionality for using fastq and bam files in the same run.

We still need a better solution for handling the HLA reference. Currently it is only possible to either process dna or rna data at the same time due to the HLA reference that has to be provided. My suggestion would be to choose the .fasta automatically based on the specified seq_type in the sample sheet AND allow users to specify custom .fasta files in the sample sheet (this might need then an additional process because of the alleles.h5 file).

In order to allow the use of different HLA references in the same run we also need to update the yara_index module and at least add the meta map to the process I guess. @apeltzer what do you think?

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• If necessary, also make a PR on the nf-core/hlatyping branch on the nf-core/test-datasets repo

[apeltzer]

Nice :)
Yes, please work on an updated yara module - we've worked on that one when modules were started so some stuff wasn't fully clear back then on how to work with it. So an update of the module would be necessary I fear.

Once you updated the module, I can review this here in detail

[apeltzer]

Please ping me on the yara module then @christopher-mohr

[christopher-mohr]

I updated the yara modules to the latest version and removed the FASTA parameter. The HLA references are now automatically set based on the given sequencing type. Not sure if there is an easier/ more elegant way for making sure that the reads are matched with the right index.

In addition I would add the possibility to provide a custom FASTA (for a specific sample) in the sample sheet in a separate PR.

[apeltzer]

Looks good to have this on DSL2 now. Some minor comments. I will also run once this is on dev to see if docs are matching expectations 👍🏻