Add ncov-recombinant v0.6.1 APHL Docker Workshop

Program_Licenses.md

@@ -74,6 +74,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Mummer | The Artistic License 2.0| https://github.com/mummer4/mummer/blob/master/LICENSE.md |
 | Mykrobe | MIT | https://github.com/Mykrobe-tools/mykrobe/blob/master/LICENSE |
 | NanoPlot | GNU GPLv3 | https://github.com/wdecoster/NanoPlot/blob/master/LICENSE |
+| ncov-recombinant | MIT | https://github.com/ktmeaton/ncov-recombinant/blob/master/LICENSE |
 | NCBI AMRFinderPlus | Public Domain | https://github.com/ncbi/amr/blob/master/LICENSE |
 | NCBI Datasets | Public Domain | https://github.com/ncbi/datasets/blob/master/pkgs/ncbi-datasets-cli/LICENSE.md |
 | NCBI table2asn | Public Domain | unknown |

README.md

@@ -99,9 +99,10 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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></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 |
-| [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></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></ul> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/katholt/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></ul> | https://github.com/wdecoster/NanoPlot |
+| [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></ul> | https://github.com/mummer4/mummer | 
+| [Mykrobe + Genotyphi](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></ul> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/katholt/genotyphi | 
+| [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></ul> | https://github.com/wdecoster/NanoPlot |
+| [ncov-recombinant](https://hub.docker.com/r/staphb/nanoplot) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncov-recombinant)](https://hub.docker.com/r/staphb/ncov-recombinant) | <ul><li>0.6.1</li></ul> | https://github.com/ktmeaton/ncov-recombinant |
 | [ngmaster](https://hub.docker.com/r/staphb/ngmaster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | <ul><li>0.5.8</li><li>1.0.0</li></ul> | https://github.com/MDU-PHL/ngmaster |
 | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) | <ul><li>13.31.0</li><li>13.35.0</li><li>13.43.2</li><li>14.0.0</li><li>14.3.0</li></ul> | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets) <br/>[https://www.ncbi.nlm.nih.gov/datasets/docs/v1/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/) |
 | [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | <ul><li>3.1.1b</li><li>3.8.4</li><li>3.8.28</li><li>3.9.3</li><li>3.9.8</li><li>3.10.1</li><li>3.10.5</li><li>3.10.16</li><li>3.10.20</li><li>3.10.24</li><li>3.10.30</li><li>3.10.36</li><li>3.10.42</li></ul> | [https://github.com/ncbi/amr](https://github.com/ncbi/amr) |
@@ -205,6 +206,7 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the
   * [@tiverson](https://github.com/tives82)
   * [@sbthandras](https://github.com/sbthandras)
   * [@idolawoye](https://github.com/idolawoye)
+  * [@whottel](https://github.com/whottel)
   * [@michellescribner](https://github.com/michellescribner)
   * [@cjjossart](https://github.com/cjjossart)
   * [@jlumpe](https://github.com/jlumpe)

ncov-recombinant/0.6.1/Dockerfile

@@ -0,0 +1,52 @@
+ARG ncov_recombinant_version='0.6.1'
+FROM mambaorg/micromamba:0.24.0 as app
+ARG ncov_recombinant_version
+USER root
+
+WORKDIR /
+
+#metadata
+LABEL base.image="FROM mambaorg/micromamba:0.24.0"
+LABEL dockerfile.version="1"
+LABEL software="ncov-recombinant"
+LABEL software.version="v${ncov_recombinant_version}"
+LABEL description="SARS-CoV-2 recombinant sequence detection"
+LABEL website="https://github.com/ktmeaton/ncov-recombinant"
+LABEL license="https://github.com/ktmeaton/ncov-recombinant/blob/master/LICENSE"
+LABEL maintainer="Wes Hottel"
+LABEL maintainer.email="wesley-hottel@uiowa.edu"
+
+#Install dependencies
+RUN apt-get update && apt-get install --no-install-recommends -y python \ 
+  git \
+  procps \
+  wget && \
+  rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+#Clone ncov-recombinant repository 
+RUN wget https://github.com/ktmeaton/ncov-recombinant/archive/refs/tags/v${ncov_recombinant_version}.tar.gz && \
+tar zxf v${ncov_recombinant_version}.tar.gz && \
+rm -rf v${ncov_recombinant_version}.tar.gz
+
+#Install ncov-recombinant
+RUN micromamba create -n ncov-recombinant-env -f /ncov-recombinant-${ncov_recombinant_version}/workflow/envs/environment.yaml &&\
+micromamba clean -a -y
+
+#Set environment
+ENV PATH="/opt/conda/envs/ncov-recombinant-env/bin:/opt/conda/envs/env/bin:${PATH}" \
+ LC_ALL=C.UTF-8
+
+WORKDIR /data
+
+#Test install using postive controls included as part of repo
+FROM app as test 
+ARG ncov_recombinant_version
+
+WORKDIR /ncov-recombinant-${ncov_recombinant_version}
+
+ENV ENV_NAME="ncov-recombinant-env"
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+RUN snakemake --profile /ncov-recombinant-${ncov_recombinant_version}/profiles/controls-positive
+
+WORKDIR /data

ncov-recombinant/0.6.1/README.md

@@ -0,0 +1,18 @@
+# ncov-recombinant container
+
+Main tool : [ncov-recombinant](https://github.com/ktmeaton/ncov-recombinant)
+
+ncov-recombinant is a recombinant sequence detection tool for SARS-CoV-2 fasta files.
+This tool:
+1) Aligns sequences and performs clade/lineage assignments with Nextclade
+2) Identifies parental clades and plots recombination breakpoints with sc2rf.
+3) Creates tables, plots, and powerpoint slides for reporting.
+
+When using this Dockerfile please make sure that you are using a WORKDIR that is mounted to your system.
+https://bioinformatics.stackexchange.com/questions/9129/access-workdir-defined-on-command-line-from-within-snakefile
+
+## Example Usage
+
+```bash
+snakemake --directory WORKDIR --profile /ncov-recombinant/profiles/controls
+```