* install seq2hla

* update schema, needs careful testing

* add sample id to publishing hierachy

* rearrange nextflow schema

* add pipeline level test for hla typing

* update docs

* bump modules version

* update rocrate

* move my beautiful new parameter ot be swallowed by tools

* retrigger test

* Update tests/hlatyping.nf.test.snap

Co-authored-by: Maxime U Garcia <[email protected]>

---------

Co-authored-by: Maxime U Garcia <[email protected]>

* update vep to 114.2

* nf-core pipelines bump-version 1.2.0dev

* fix tests and update CHANGELOG

* fix linting

* update CHANGELOG

* fix prepare_genome tests

* Update subworkflows/local/vcf_annotate_all/main.nf

Co-authored-by: James A. Fellows Yates <[email protected]>

* allow for annotation cache cloud hosting outside of annotation-cache

* remove workflow.trace calls

* first step of prepare_genome refactor

* gtf gff

* exon_bed

* simplify prepare_genome

* restore names properly

* remove fromPath

* fix calls

* handles more than 1 vcf for dbsnp and known indels

* remove workflow.trace call

* fix collect

* fix typo

* maximize prepare_genome

* minor polish

* re-generate snapshot

* sort tests output so that snapshot is sorted

* move versions + fix collect

* update snapshots

* assert success of failure early

* no need for quay.io

---------

Co-authored-by: James A. Fellows Yates <[email protected]>

* nf-core pipelines bump-version 1.2.0

* update CHANGELOG

* Update CHANGELOG.md

* update README

* update docs

* update CHANGELOG

* fix rocrate

* update CHANGELOG

* fix test_full

* no need for this

* update CHANGELOG

* update vep_cache

* simplify launching rnavar subworkflow

* minor polish

* update schema

* fix schema

* fix typo + update CHANGELOG

Release 1.2.0