Dockerfile

FROM ubuntu:jammy as app

ARG FASTP_VER="0.23.4"

LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="Fastp"
LABEL software.version=$FASTP_VER
LABEL description="An ultra-fast all-in-one FASTQ preprocessor"
LABEL website="https://github.com/OpenGene/fastp"
LABEL license="https://github.com/OpenGene/fastp/blob/master/LICENSE"
LABEL maintainer="Idowu Olawoye"
LABEL maintainer.email="olawoyei0303@run.edu.ng"
LABEL maintainer2="Erin Young"
LABEL maintainer2.email="eriny@utah.gov"

RUN apt-get update && apt-get install -y --no-install-recommends \
  wget \
  ca-certificates && \
  apt-get autoclean && rm -rf /var/lib/apt/lists/*

RUN mkdir fastp && \
  cd fastp && \ 
  wget http://opengene.org/fastp/fastp.${FASTP_VER} && \
  mv fastp.${FASTP_VER} fastp && \
  chmod a+x ./fastp && \
  mkdir /data
 
ENV PATH="/fastp:$PATH"

WORKDIR /data

CMD [ "fastp", "--help" ]

# A second FROM insruction creates a new stage
# We use `test` for the test image
FROM app as test

# downloading sars-cov-2 fastq test files
RUN wget https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \
wget https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz

# running fastp on the files
RUN fastp \
        -i SRR13957123_1.fastq.gz \
        -I SRR13957123_2.fastq.gz \
        -o SRR13957123_PE1.fastq.gz \
        -O SRR13957123_PE2.fastq.gz \
        -h SRR13957123_fastp.html \
        -j SRR13957123_fastp.json