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Merge pull request #146 from CDCgov/v2.1.1-dev
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v2.1.1 dev merge to main
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nvlachos authored Mar 25, 2024
2 parents 0129b41 + 02ea21b commit 5a5a7a5
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55 changes: 55 additions & 0 deletions .github/workflows/update_clone_badge.yml
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name: Update Clone Badge

on:
schedule:
- cron: '0 0 * * *' # Runs at midnight every day

jobs:
update-badge:
runs-on: ubuntu-latest
if: github.ref == 'refs/heads/v2.2.0-dev' # Run only on v2.2.0-dev branch

steps:
- name: Checkout repository
uses: actions/checkout@v2
with:
token: ${{ secrets.GH_ACTION }}
ref: v2.2.0-dev # Specify the branch to checkout

- name: Get clone count for today

id: get_clone_count
run: |
# Fetch clone count from GitHub API for today
CLONE_COUNT=$(curl -s -H "Authorization: Bearer ${{ secrets.GH_ACTION }}" \
"https://api.github.com/repos/CDCgov/phoenix/traffic/clones" | jq -r --arg target_day "$(date -d yesterday +%Y-%m-%d)" '.clones[] | select(.timestamp | startswith($target_day))' | jq -r '.count')
echo "CLONE_COUNT=$CLONE_COUNT" >> $GITHUB_ENV
- name: Extract previous clone count from README
id: extract_previous_count
run: |
# Extract previous clone count from README.md
PREVIOUS_COUNT=$(grep -oP '(?<=Clones%3A%20)\d+' README.md)
echo "PREVIOUS_COUNT=$PREVIOUS_COUNT" >> $GITHUB_ENV
- name: Calculate new total clone count
if: ${{ env.PREVIOUS_COUNT != env.NEW_TOTAL }}
id: calculate_new_total
run: |
# Calculate new total clone count by adding today's count to previous count
NEW_TOTAL=$((PREVIOUS_COUNT + CLONE_COUNT))
echo "NEW_TOTAL=$NEW_TOTAL" >> $GITHUB_ENV
- name: Update README badge
if: ${{ env.PREVIOUS_COUNT != env.NEW_TOTAL }}
run: |
sed -i -E "s/Clones%3A%20[0-9]+/Clones%3A%20${{ env.NEW_TOTAL }}/g" README.md
- name: Commit and push changes
if: ${{ env.PREVIOUS_COUNT != env.NEW_TOTAL }}
run: |
git config --local user.email "[email protected]"
git config --local user.name "HAISeq"
git add README.md
git commit -m "Update clone and download counts"
git push
21 changes: 21 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -243,3 +243,24 @@ Below are the list of changes to phx since is initial release. As fixes can take
- [ARG-ANNOT](http://backup.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/2041/arg-annot-v4-aa-may2018_doc.fasta) hasn't changed since the last time the database was created and contains updates since version [NT v6 July 2019](https://www.mediterranee-infection.com/acces-ressources/base-de-donnees/arg-annot-2/)
- [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/)
- Includes until 2024-01-28 [commit 97d1fe0cd0a119172037f6bdb29f8a1c7c6e6019](https://bitbucket.org/genomicepidemiology/resfinder_db/commits/branch/master)

## [v2.1.1](https://github.com/CDCgov/phoenix/releases/tag/v2.1.1) (03/25/2024)

**Implemented Enhancements:**
- The following OXA genes were added to be highlighted as blaOXA-48 like in the griphin summary: "blaOXA-1167","blaOXA-1181","blaOXA-1200","blaOXA-1201","blaOXA-1205","blaOXA-1207","blaOXA-1211","blaOXA-1212","blaOXA-1213".

**Fixed Bugs:**
- Fix for issue [#130](https://github.com/CDCgov/phoenix/issues/130) Identified when an Isolate is incorrectly assigned to cronobacter scheme when it should have been ecloacae. Extension of larger scoring problem with MLST-2.23.0.
- Fixed [#142](https://github.com/CDCgov/phoenix/issues/142) where names with multiple instances of "R2" in their name couldn't be parsed properly and don't move past the corruption check step. [commit `7fc0ac3c026b7c12608be4dd1d3682675e31d0fe`](https://github.com/CDCgov/phoenix/commit/7fc0ac3c026b7c12608be4dd1d3682675e31d0fe)
- Fixed an issue in FASTANI. The file for checking 80%+ identity could not be found because the DB_Version was not set when "No Mash Hits found" occurs.
- Updated amrfinderplus container from BLAST v2.14.0 --> v2.15.0 to fix [#144](https://github.com/CDCgov/phoenix/issues/144).

**Container Updates:**
- Containers updated to include developers bug fixes:
- amrfinderplus: v3.11.26 to v3.12.8 which has [changes on how AR genes are called](https://github.com/ncbi/amr/releases/tag/amrfinder_v3.12.8).

**Database Updates:**
- Curated AR gene database was updated on 2024-02-29 (yyyy-mm-dd) to include the new AMRFinder database:
- [AMRFinderPlus database](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/)
- Version [2024-01-31.1](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/3.12/)
- [ARG-ANNOT](http://backup.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/2041/arg-annot-v4-aa-may2018_doc.fasta) and [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/) haven't changed since last version release.
14 changes: 9 additions & 5 deletions README.md
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# :fire::bird::fire: PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

<!-- [![GitHub Downloads](https://img.shields.io/github/downloads/CDCgov/phoenix/total.svg?style=social&logo=github&label=Download)](https://github.com/CDCgov/phoenix/releases) -->
<!-- [![GitHub Downloads](https://img.shields.io/github/downloads/cdcgov/phoenix/total.svg?style=social[![GitHub Downloads](https://img.shields.io/github/downloads/CDCgov/phoenix/total.svg?style=social&logo=github&label=Download-) -->

[![DOI](https://zenodo.org/badge/490844937.svg)](https://zenodo.org/badge/latestdoi/490844937)

[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2Fcdcgov%2Fphoenix&count_bg=%233DC8A9&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=Page+Hits&edge_flat=false)](https://hits.seeyoufarm.com)

[![GitHub Downloads](https://img.shields.io/github/downloads/cdcgov/phoenix/total.svg?style=social&logo=github&label=Download)](https://github.com/cdcgov/phoenix/releases)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

[![Get help on Slack](http://img.shields.io/badge/slack-StaPH--B%20%23phoenix--dev-4A154B?labelColor=000000&logo=slack)](https://staph-b-dev.slack.com/channels/phoenix-dev)

#### Metrics

[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2Fcdcgov%2Fphoenix&count_bg=%233DC8A9&title_bg=%23555555&icon=&icon_color=%23E7E7E7&title=Page+Hits&edge_flat=false)](https://hits.seeyoufarm.com)

<!--- ![GitHub Clones](https://img.shields.io/github/downloads/cdcgov/phoenix/total.svg?style=social&logo=github&label=Clones-) --->

[![Custom Badge](https://img.shields.io/badge/GitHub-%F0%9F%94%A5%F0%9F%90%A6%F0%9F%94%A5%20GitHub%20Clones%3A%20262-blue?logo=GitHub&style=for-the-badge&logoColor=black&label=%20&labelColor=white&color=blue&style=flat-square)](https://github.com/)

For full documentation on the pipeline see the [Wiki](https://github.com/cdcent/phoenix/wiki), but quick start instructions are provided below if you are feeling brave.

# Quick Start
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