Merge pull request #801 from hutchinsonmiri/master

Adding MultiQC version 1.17

README.md

@@ -187,7 +187,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [minipolish](https://hub.docker.com/r/staphb/minipolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | <ul><li>0.1.3</li></ul> | https://github.com/rrwick/Minipolish |
 | [mlst](https://hub.docker.com/r/staphb/mlst) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mlst)](https://hub.docker.com/r/staphb/mlst) | <ul><li>2.16.2</li><li>2.17.6</li><li>2.19.0</li><li>2.22.0</li><li>2.22.1</li><li>2.23.0</li><li>[2.23.0-2023-07 (databases updated July 2023)](mlst/2.23.0-2023-07/)</li><li>[2.23.0-2023-08 (databases updated Aug 2023)](mlst/2.23.0-2023-08/)</li></ul> | https://github.com/tseemann/mlst |
 | [Mugsy](https://hub.docker.com/r/staphb/mugsy) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mugsy)](https://hub.docker.com/r/staphb/mugsy) | <ul><li>1r2.3</li></ul> | http://mugsy.sourceforge.net/ |
-| [MultiQC](https://hub.docker.com/r/staphb/multiqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | <ul><li>1.7</li><li>1.8</li></ul> | https://github.com/ewels/MultiQC |
+| [MultiQC](https://hub.docker.com/r/staphb/multiqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | <ul><li>1.7</li><li>1.8</li><li>[1.18](./multiqc/1.18/)</li></ul> | https://github.com/ewels/MultiQC |
 | [Mummer](https://hub.docker.com/r/staphb/mummer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mummer)](https://hub.docker.com/r/staphb/mummer) | <ul><li>4.0.0</li><li>4.0.0 + RGDv2</li><li>4.0.0 + RGDv2 + gnuplot</li></ul> | https://github.com/mummer4/mummer |
 | [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | <ul><li>0.11.0 (Mykrobe) & 1.9.1 (Genotyphi) </li><li>0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping) </li><li>0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) </li><li>[0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](mykrobe/0.12.2/)</li><li>[0.13.0](./mykrobe/0.13.0)</li></ul> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/typhoidgenomics/genotyphi <br/> https://github.com/katholt/sonneityping |
 | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | <ul><li>1.27.0</li><li>1.29.0</li><li>1.30.1</li><li>1.32.0</li><li>1.33.0</li><li>1.40.0</li><li>[1.41.6](nanoplot/1.41.6/)</li></ul> | https://github.com/wdecoster/NanoPlot |

multiqc/1.18/Dockerfile

@@ -0,0 +1,60 @@
+FROM ubuntu:jammy as app
+
+ARG MULTIQC_VER="1.18"
+
+# metadata
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="MultiQC"
+LABEL software.version="${MULTIQC_VER}"
+LABEL description="Aggregate bioinformatics results across many samples into a single report."
+LABEL website="https://github.com/ewels/MultiQC"
+LABEL license="https://github.com/ewels/MultiQC/blob/master/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+# Although... let's be honest. Most of this is copied and pasted from Abigail Shockey
+
+# install remaining dependencies
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y \
+    wget \
+    git \
+    python3 \
+    python3-dev \
+    python3-pip \
+    locales \
+    pandoc \
+    texlive-xetex && \
+    locale-gen en_US.UTF-8 && \
+    apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install multiqc
+RUN pip3 install "multiqc==${MULTIQC_VER}"
+
+
+# add pandoc to path
+ENV PATH="${PATH}" \
+    LC_ALL='C.UTF-8' LANG='C.UTF-8'
+
+CMD multiqc --help
+
+RUN mkdir /data
+WORKDIR /data
+
+# testing layer starts here
+FROM app as test
+
+# to ensure multiqc is in PATH
+RUN multiqc --help
+
+# set working directory so that all test inputs & outputs are kept in /test
+RUN mkdir /test
+WORKDIR /test
+
+# getting multiqc test data and testing pandoc
+RUN git clone https://github.com/ewels/MultiQC_TestData && \
+    multiqc . && \
+    ls multiqc_report.html 
+
+RUN multiqc /test/MultiQC_TestData/data/modules/BUSCO --filename multiqc_report2.html -o multiqc_data2 --pdf && \
+    ls multiqc_data2/multiqc_report2.html multiqc_data2/multiqc_report2_data

multiqc/1.18/README.md

@@ -0,0 +1,13 @@
+# MultiQC container
+
+Main tool : [MultiQC](https://multiqc.info/)
+
+Aggregate results from bioinformatics analyses across many samples into a single report.
+
+Full documentation: [Docs] (https://multiqc.info/docs/)
+
+# Example Usage
+
+```
+multiqc -f --cl_config "prokka_fn_snames: True"  .
+```