Releases: Kincekara/C-BIRD
Releases · Kincekara/C-BIRD
v1.6.0
Updates:
- 💻 AmrFinderPlus: staphb/ncbi-amrfinderplus:3.12.8-2024-01-31.1 -> staphb/ncbi-amrfinderplus:3.12.8-2024-05-02.2
- 📜 DB: 2024-01-31.1 -> 2024-05-02.2
- 💻 BUSCO: 5.6.1 -> 5.7.1
- 📜 DB: 2024-01-08
- 💻 MLST: staphb/mlst:2.23.0-2024-01 -> staphb/mlst:2.23.0-2024-05-01
- 📜 PubMLST update May 2024
- 📜 Kraken 2 / Bracken Refseq indexes: Standard-8 2024-01-12
v1.5.1
v1.5.0
Updates:
- 💻 AmrFinderPlus: 3.11.26 -> 3.12.8
- 📜 DB: 2023-11-15.1 -> 2024-01-31.1
- 💻 Cbird-Util: v1.0 -> v1.1
- 🐛 fix coverage and identity calculation, and rounding for target gene search in report_generator.py
- 💻 QUAST: kincekara/quast:5.2.0-light -> staphb/quast:5.2.0-slim
v1.4.0
Updates:
- 💻 AmrFinderPlus: 3.11.20 -> 3.11.26
- 📜 DB: 2023-09-26.1 -> 2023-11-15.1
- 💻 BBtools: 39.03 -> 39.06
- 💻 Blast+: 2.14.0 -> 2.15.0
- 💻 BUSCO: 5.4.7 -> 5.6.1
- 📜 Kraken 2 / Bracken Refseq indexes: Standard-8 2023-10-09
- 💻 MLST: staphb/mlst:2.23.0-2023-08 -> staphb/mlst:2.23.0-2024-01
- 📜 PubMLST update January 2024
v1.3.0
🐤 Small databases and files are added in the docker containers in this release. So, installing and setting up the workflow will be much easier. In addition to reads, only the kraken2 database and custom c-bird mash sketch are needed now.
Although these changes make the workflow more restrictive, it suits its validation easy pipeline purpose.
Updates:
- 💻 AmrFinderPlus: 3.11.18 -> 3.11.20
- 📜 DB: 2023-08-08.2 -> 2023-09-26.1
- 💻 BBtools: 39.01 -> 39.03
- 💻 Bracken 2.8 -> 2.9
Changes:
🔧 Auto trimming length value according to read length for scaffold trimming
🔧 StaphB docker containers where available
🔧 Estimated sequencing depth from trimmed reads was added
🔧 Small code changes in the workflow to apply the modifications above
v1.2.1
🐤 This release includes MLST database update and minor changes.
Updates:
- 💻 MLST docker container: staphb/mlst:2.23.0 -> staphb/mlst:2.23.0-2023-08
- 📜 database update August 2023
Changes:
- 🔧 Scaffolds trimming default threshold is set to 300 bp
- 🐛 Fix parsing bug in plasmidfinder task
v1.1.0
🐤 This release mainly includes the program/tool updates.
Updates:
- 💻 AmrFinderPlus: 3.10.40 -> 3.11.18
- 📜 DB: 2022-10-11.2 -> 2023-08-08.2
- 💻 BBtools: 38.98 -> 39.01
- 💻 Blast+: 2.13.0 -> 2.14.0
- 💻 BUSCO: 5.4.3 -> 5.4.7
- 💻 FastP: 0.23.2 -> 0.23.4
- 💻 QUAST: 5.0.2 -> 5.2.0
- 💻 Kraken2: 2.1.2 -> 2.1.3
Code changes:
- 🔧 Necessary changes related to curated organisms in AmrFinderPlus.