From 0de36b7a1675927fdc9c09ae4991fa6df906a13d Mon Sep 17 00:00:00 2001 From: Kincekara Date: Tue, 10 Dec 2024 18:30:36 +0000 Subject: [PATCH] adds fastp 0.24.0 --- README.md | 2 +- fastp/0.24.0/Dockerfile | 46 +++++++++++++++++++++++++++++++++++++++++ fastp/0.24.0/README.md | 13 ++++++++++++ 3 files changed, 60 insertions(+), 1 deletion(-) create mode 100644 fastp/0.24.0/Dockerfile create mode 100644 fastp/0.24.0/README.md diff --git a/README.md b/README.md index 4e9c58238..417aa68f5 100644 --- a/README.md +++ b/README.md @@ -162,7 +162,7 @@ To learn more about the docker pull rate limits and the open source software pro | [EToKi](https://hub.docker.com/r/staphb/etoki)
[![docker pulls](https://badgen.net/docker/pulls/staphb/etoki)](https://hub.docker.com/r/staphb/etoki) | | https://github.com/zheminzhou/EToKi | | [FastANI](https://hub.docker.com/r/staphb/fastani)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | | https://github.com/ParBLiSS/FastANI | | [fasten](https://hub.docker.com/r/staphb/fasten)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fasten)](https://hub.docker.com/r/staphb/fasten) | | https://github.com/lskatz/fasten | -| [Fastp](https://hub.docker.com/r/staphb/fastp)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastp)](https://hub.docker.com/r/staphb/fastp) | | http://opengene.org/fastp/
https://github.com/OpenGene/fastp | +| [Fastp](https://hub.docker.com/r/staphb/fastp)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastp)](https://hub.docker.com/r/staphb/fastp) | | http://opengene.org/fastp/
https://github.com/OpenGene/fastp | | [FastTree](https://hub.docker.com/r/staphb/fasttree)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | | http://www.microbesonline.org/fasttree/ | | [FastQC](https://hub.docker.com/r/staphb/fastqc)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/s-andrews/FastQC | | [fastq-scan](https://hub.docker.com/r/staphb/fastq-scan)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastq-scan)](https://hub.docker.com/r/staphb/fastq-scan) | | https://github.com/rpetit3/fastq-scan | diff --git a/fastp/0.24.0/Dockerfile b/fastp/0.24.0/Dockerfile new file mode 100644 index 000000000..d847f9813 --- /dev/null +++ b/fastp/0.24.0/Dockerfile @@ -0,0 +1,46 @@ +FROM ubuntu:jammy as app + +ARG FASTP_VER="0.24.0" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="Fastp" +LABEL software.version=${FASTP_VER} +LABEL description="An ultra-fast all-in-one FASTQ preprocessor" +LABEL website="https://github.com/OpenGene/fastp" +LABEL license="https://github.com/OpenGene/fastp/blob/master/LICENSE" +LABEL maintainer="Idowu Olawoye" +LABEL maintainer.email="olawoyei0303@run.edu.ng" +LABEL maintainer2="Erin Young" +LABEL maintainer2.email="eriny@utah.gov" + +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget --no-check-certificate -O /usr/local/bin/fastp http://opengene.org/fastp/fastp.${FASTP_VER} && \ + chmod a+x /usr/local/bin/fastp + +ENV LC_ALL=C + +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 -q --no-check-certificate \ + https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz \ + 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 diff --git a/fastp/0.24.0/README.md b/fastp/0.24.0/README.md new file mode 100644 index 000000000..c3674c358 --- /dev/null +++ b/fastp/0.24.0/README.md @@ -0,0 +1,13 @@ +# fastp container + +Main tool : [fastp](https://github.com/OpenGene/fastp) + +Full documentation: https://github.com/OpenGene/fastp + +> A tool designed to provide fast all-in-one preprocessing for FastQ files. + +## Example Usage + +```bash +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 +```