adds fastp 0.24.0

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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/etoki)](https://hub.docker.com/r/staphb/etoki) | <ul><li>1.2.1</li></ul> | https://github.com/zheminzhou/EToKi |
 | [FastANI](https://hub.docker.com/r/staphb/fastani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | <ul><li>1.1</li><li>1.32</li><li>1.33</li><li>1.33 + RGDv2</li><li>[1.34](fastani/1.34)</li><li>[1.34 + RGDv2](fastani/1.34-RGDV2/)</li></ul> | https://github.com/ParBLiSS/FastANI |
 | [fasten](https://hub.docker.com/r/staphb/fasten) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fasten)](https://hub.docker.com/r/staphb/fasten) | <ul><li>[0.7.2](./fasten/0.7.2)</li><li>[0.8.1](./fasten/0.8.1/)</li></ul> | https://github.com/lskatz/fasten |
-| [Fastp](https://hub.docker.com/r/staphb/fastp) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastp)](https://hub.docker.com/r/staphb/fastp) | <ul><li>0.23.2</li><li>[0.23.4](fastp/0.23.4/)</li></ul> | http://opengene.org/fastp/ <br/> https://github.com/OpenGene/fastp |
+| [Fastp](https://hub.docker.com/r/staphb/fastp) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastp)](https://hub.docker.com/r/staphb/fastp) | <ul><li>0.23.2</li><li>[0.23.4](fastp/0.23.4/)</li><li>[0.24.0](./fastp/0.24.0/)</li></ul> | http://opengene.org/fastp/ <br/> https://github.com/OpenGene/fastp |
 | [FastTree](https://hub.docker.com/r/staphb/fasttree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | <ul><li>2.1.11</li></ul> | http://www.microbesonline.org/fasttree/ |
 | [FastQC](https://hub.docker.com/r/staphb/fastqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | <ul><li>0.11.8</li><li>0.11.9</li><li>0.12.1</li></ul> | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ <br/> https://github.com/s-andrews/FastQC |
 | [fastq-scan](https://hub.docker.com/r/staphb/fastq-scan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastq-scan)](https://hub.docker.com/r/staphb/fastq-scan) | <ul><li>0.4.3</li><li>0.4.4</li><li>1.0.0</li><li>1.0.1</li></ul> | https://github.com/rpetit3/fastq-scan |

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=${FASTP_VER}
+LABEL description="An ultra-fast all-in-one FASTQ preprocessor"
+LABEL website="https://github.com/OpenGene/fastp"
+LABEL license="https://github.com/OpenGene/fastp/blob/master/LICENSE"
+LABEL maintainer="Idowu Olawoye"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Erin Young"
+LABEL maintainer2.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate -O /usr/local/bin/fastp http://opengene.org/fastp/fastp.${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

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
+```