Till Hartmann

In our rust version of hgvs, I stumbled upon cases where the interval requested in `get_altered_sequence` does not agree with the location range in the variant description. However, I suspect...

feat: add mehari wrappers

1

This PR adds wrappers for mehari: - `annotate-seqvars` for annotating VCF/VCF.gz/BCF (sequence variants, SNVs, indels, _excluding_ structural variants) - `download-transcript-db` for downloading transcript databases required for annotation of SO terms...

I think neither pysam nor cyvcf2 support VCF >=4.4 yet, and will choke on GT strings with complete phasing information, e.g. `/0/1` or `|1/0`.

fix: always update pins on `update-conda-envs --pin-envs`

1

During `update-conda-envs --pin-envs environment.yaml`, if the environment.yaml has no changes (e.g. if completely unconstrained), the pins would never be touched, even though there will likely be newer versions that fulfill...

… use aliases (from biocommons bioutils ASSEMBLY_INFO) instead.

feat: allow setting launchDir in params

7

Because nextflow does not allow specifying the `launchDir`, but stores its `.nextflow` folder in that directory, the wrapper now allows changing into the directory specified in the param `launch_dir` before...

fix: add version constraint to utils/nextflow env yaml

3

As a less invasive alternative to https://github.com/snakemake/snakedeploy/pull/107 this PR adds a version constraint to the nextflow version in the environment.yaml so `snakedeploy update-conda-envs --pin-envs` can actually pick up changes. ##...

Include splicing terms as children of coding_transcript_intron_variant

3

Right now, the following splice related terms - [splice_acceptor_variant](http://www.sequenceontology.org/browser/current_release/term/SO:0001574) - [splice_donor_5th_base_variant](http://www.sequenceontology.org/browser/current_release/term/SO:0001787) - [splice_donor_variant](http://www.sequenceontology.org/browser/current_release/term/SO:0001575) - (and their children) are children of `splice_site_variant`, which in turn is a child of `intron_variant`. However,...