Skip to content

Commit

Permalink
Merge pull request #754 from uclahs-cds/czhu-add-badges
Browse files Browse the repository at this point in the history
Version bump to 1.0.0 and documentation updated
  • Loading branch information
zhuchcn authored Jun 20, 2023
2 parents d6b6092 + 0caf577 commit 0c8489d
Show file tree
Hide file tree
Showing 4 changed files with 10 additions and 3 deletions.
2 changes: 1 addition & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm

## [Unreleased]

## [0.12.0] - 2023-04-18
## [1.0.0] - 2023-06-15

### Added

Expand Down
5 changes: 4 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,11 @@

<!-- badges: start -->

[![Lifecycle:Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)
[![Tests](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml)
[![Docs](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/docs.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/docs.yaml)
[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/private-moPepGen/pkgs/container/mopepgen)
[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](https://uclahs-cds.github.io/private-moPepGen/)
[![License](https://img.shields.io/badge/License-GPL_v2-blue)](./LICENSE.txt)

<!-- badges: end -->

Expand Down
4 changes: 4 additions & 0 deletions docs/vignette.md
Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,10 @@ Single nucleotide variants (SNVs/SNPs) and small insertions/deletions (INDELs) c

Note that, the VEP cache files must be downloaded prior to running VEP (see [here](https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html)). The VEP developers recommend downloading the VEP cache version which corresponds to the Ensembl VEP installation. We also strongly recommend explicitly providing the exact reference genome and GTF file used in moPepGen to VEP to ensure the consistency of transcript IDs (i.e., using `--custom ${ANNOTATION_GTF},${REFERENCE_VERSION},gtf`). The exact genome FASTA and annotation GTF files should be used later when calling for variant peptides.

!!! warning

If you use `--chr` to limit the chromosomes to annotate, make sure the style matches with your VCF/BED file. For example, if the chromosomes have the 'chr' prefix in your VCF file (*i.e.*, chr1, chr2, ...), you must include the prefix as well (*i.e.*, `--chr chr1,chr2,chr3`).

The example data does not work for VEP.

```shell
Expand Down
2 changes: 1 addition & 1 deletion moPepGen/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
from typing import Iterable, IO


__version__ = '0.12.0'
__version__ = '1.0.0'

## Error messages
ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'
Expand Down

0 comments on commit 0c8489d

Please sign in to comment.