diff ./build-files/bracken/2.9/Dockerfile ./build-files/bracken/3.1/Dockerfile
2c2
< ARG BRACKEN_VER="2.9"
---
> ARG BRACKEN_VER="3.1"
5c5
< FROM ubuntu:jammy as builder
---
> FROM ubuntu:jammy AS builder
10c10,14
< RUN apt-get update && apt-get install -y build-essential perl wget zlib1g-dev
---
> RUN apt-get update && apt-get install -y \
>     build-essential \
>     perl \
>     wget \
>     zlib1g-dev
13c17
< RUN wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v${KRAKEN_VER}.tar.gz &&\
---
> RUN wget -q https://github.com/DerrickWood/kraken2/archive/refs/tags/v${KRAKEN_VER}.tar.gz &&\
18c22
< RUN wget https://github.com/jenniferlu717/Bracken/archive/refs/tags/v${BRACKEN_VER}.tar.gz &&\
---
> RUN wget -q https://github.com/jenniferlu717/Bracken/archive/refs/tags/v${BRACKEN_VER}.tar.gz &&\
24c28
< FROM ubuntu:jammy as app
---
> FROM ubuntu:jammy AS app
38,39c42,47
< RUN apt-get update && apt-get install --no-install-recommends -y perl python-is-python3 libgomp1 pigz \
< && rm -rf /var/lib/apt/lists/* && apt-get autoclean
---
> RUN apt-get update && apt-get install --no-install-recommends -y \
>     perl \
>     python-is-python3 \
>     libgomp1 \
>     pigz &&\
>     rm -rf /var/lib/apt/lists/* && apt-get autoclean
44,45c52,53
< ENV LC_ALL=C
< ENV PATH="${PATH}:/kraken2:/Bracken"
---
> ENV PATH="${PATH}:/kraken2:/Bracken" \
>     LC_ALL=C
52c60
< FROM app as test
---
> FROM app AS test
54c62
< RUN apt-get update && apt-get install --no-install-recommends -y wget
---
> RUN apt-get update && apt-get install -y wget
57c65
< RUN wget --no-check-certificate https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20231009.tar.gz && \
---
> RUN wget -q https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20231009.tar.gz && \
61c69
< RUN wget --no-check-certificate https://github.com/StaPH-B/docker-builds/raw/83ee344304794f4ffa162d1c082bb35f916badcf/tests/SARS-CoV-2/SRR13957123_1.fastq.gz \
---
> RUN wget -q https://github.com/StaPH-B/docker-builds/raw/83ee344304794f4ffa162d1c082bb35f916badcf/tests/SARS-CoV-2/SRR13957123_1.fastq.gz \
66c74
< RUN bracken -d ./db -i k2_report.txt -o bracken_report.txt -r 75 -l S -t 10 && \
---
> RUN bracken -d ./db -i k2_report.txt -o bracken_report.txt -r 75 -l S -t 10 &&\