Allow poorpipe long read sequencing uploads

[dnil]

Similar to #3993 - which appears stale atm. Development is in parallel on several pipes, but we have some data from https://github.com/J35P312/poorpipe so it sails up as the first to fix. Several issues are likely to be similar.

Let's do a MVP first, with just allowing uploads with the current VEP version annotation. That will be needed for e.g. the NF-core rare-disease soon as well. The data I have from poorpipe is VEP 107, and the NF-core dev is VEP 110.

A couple of obvious things:

• gnomad frequency key appears to have changed
• (we have a new VAF FORMAT field - will be esp nice for somatic data)

Dev data available on e.g. /home/proj/development/rare-disease/ONT/analysis/poorpipe/2023-34375-05/

[dnil]

Testing an upload, after some hardfiltering and genmod:ding.

2024-02-01 22:29:54 hasta.scilifelab.se scout.adapter.mongo.variant_loader[196268] INFO Nr variants parsed: 502435
2024-02-01 22:29:54 hasta.scilifelab.se scout.adapter.mongo.variant_loader[196268] INFO Nr variants inserted: 25473
2024-02-01 22:29:54 hasta.scilifelab.se scout.adapter.mongo.variant_loader[196268] DEBUG Nr bulks inserted: 8472
2024-02-01 22:29:54 hasta.scilifelab.se scout.adapter.mongo.variant_loader[196268] INFO Updating variant_rank for all variants
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.variant_loader[196268] INFO Updating variant_rank done
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] DEBUG didn't find vcf_sv, skipping
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] DEBUG didn't find vcf_cancer, skipping
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] DEBUG didn't find vcf_cancer_sv, skipping
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] DEBUG didn't find vcf_str, skipping
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] DEBUG didn't find vcf_mei, skipping
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] DEBUG didn't find vcf_fusion, skipping
2024-02-01 22:30:03 hasta.scilifelab.se scout.adapter.mongo.case[196268] INFO Loading case F0056610 into database

[dnil]

This looks like Nanopore allright (https://scout-stage.scilifelab.se/cust002/F0056610):

Good enough! 😸

[dnil]

Now also a tentative SV view:
https://scout-stage.scilifelab.se/cust002/F0057045

[dnil]

As soon as we have tags for them, add new callers:

SV

• sniffles, sniffles2
• CNVpytor

STR

• trgt