preprocessing v3.0.1 release (#171)

* Update nf-teams plugin version to 0.1.1

* back to dev

* bump modules

* add parameter typing

* fix lint and bump nextflow

* bump nf-test to strict syntax compatible version

* fix fastq_to_aligned_cram

* don't use params in subworkflows

* fix mosdepth env issue on gcp (#166)

* fix mosdepth env issue on gcp

* fix tests

* bump tests

* bump mosdepth

* bump nf-test

* add csi index to unstable keys

* update changelog

* revert nf-test bump

* update snaps

---------

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* add pixi env

* fix tests

* pre-commit

* address review comments

* recreate lock file for platforms + disable nextflow telemetry

* Bump/template (#168)

* bump nf-core version

* fix files_unchanged

* bump modules

* drop custom registries in config

* fix nf linting

* fix nf-core linting

* changelog

* fix tests

* fix nf-core linting

* fix available genomes

* update plugins and default params

* fix falco issues (#170)

* changelog

* fix snp samples rg

* fix falco

* fix commented tests

* bump version number

---------

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>

Author: matthdsm

ro-crate-metadata.json

@@ -345,4 +345,4 @@
             "url": "https://github.com/nvnieuwk"
         }
     ]
-}
+}