From 7eaf78329936ca47315ace8d17b6f518d26683dd Mon Sep 17 00:00:00 2001 From: Young Date: Mon, 30 Sep 2024 11:45:59 -0600 Subject: [PATCH] adding multiqc version 1.25 (#1062) --- README.md | 2 +- multiqc/1.25/Dockerfile | 47 +++++++++++++++++++++++++++++++++++++++++ multiqc/1.25/README.md | 13 ++++++++++++ 3 files changed, 61 insertions(+), 1 deletion(-) create mode 100644 multiqc/1.25/Dockerfile create mode 100644 multiqc/1.25/README.md diff --git a/README.md b/README.md index f0c5d67ce..178e12394 100644 --- a/README.md +++ b/README.md @@ -212,7 +212,7 @@ To learn more about the docker pull rate limits and the open source software pro | [minipolish](https://hub.docker.com/r/staphb/minipolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | | https://github.com/rrwick/Minipolish | | [mlst](https://hub.docker.com/r/staphb/mlst)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mlst)](https://hub.docker.com/r/staphb/mlst) | | https://github.com/tseemann/mlst | | [Mugsy](https://hub.docker.com/r/staphb/mugsy)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mugsy)](https://hub.docker.com/r/staphb/mugsy) | | http://mugsy.sourceforge.net/ | -| [MultiQC](https://hub.docker.com/r/staphb/multiqc)
[![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | | https://github.com/MultiQC/MultiQC | +| [MultiQC](https://hub.docker.com/r/staphb/multiqc)
[![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | | https://github.com/MultiQC/MultiQC | | [Mummer](https://hub.docker.com/r/staphb/mummer)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mummer)](https://hub.docker.com/r/staphb/mummer) | | https://github.com/mummer4/mummer | | [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | | https://github.com/Mykrobe-tools/mykrobe
https://github.com/typhoidgenomics/genotyphi
https://github.com/katholt/sonneityping | | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | | https://github.com/wdecoster/NanoPlot | diff --git a/multiqc/1.25/Dockerfile b/multiqc/1.25/Dockerfile new file mode 100644 index 000000000..4e0fd9953 --- /dev/null +++ b/multiqc/1.25/Dockerfile @@ -0,0 +1,47 @@ +FROM ubuntu:jammy as app + +ARG MULTIQC_VER="1.25" + +# metadata +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="MultiQC" +LABEL software.version="${MULTIQC_VER}" +LABEL description="Aggregate bioinformatics results across many samples into a single report." +LABEL website="https://github.com/MultiQC/MultiQC" +LABEL license="https://github.com/MultiQC/MultiQC/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + python3-pip && \ + apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install multiqc +RUN pip3 install --no-cache-dir -vv "multiqc==${MULTIQC_VER}" + +ENV 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 + +# getting git +RUN apt-get update && apt-get install -y git + +# 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 +RUN git clone https://github.com/ewels/MultiQC_TestData && \ + multiqc . && \ + ls multiqc_report.html diff --git a/multiqc/1.25/README.md b/multiqc/1.25/README.md new file mode 100644 index 000000000..879cb9cd8 --- /dev/null +++ b/multiqc/1.25/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" . +```