Merge pull request #1050 from Kincekara/verkko

adds verkko v2.2

README.md

@@ -299,7 +299,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Trycycler](https://hub.docker.com/r/staphb/trycycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trycycler)](https://hub.docker.com/r/staphb/trycycler) | <ul><li>[0.3.1](./trycycler/0.3.1/)</li><li>[0.3.2](./trycycler/0.3.2/)</li><li>[0.3.3](./trycycler/0.3.3/)</li><li>[0.5.0](./trycycler/0.5.0/)</li><li>[0.5.3](./trycycler/0.5.3/)</li><li>[0.5.4](./trycycler/0.5.4/)</li><li>[0.5.5](./trycycler/0.5.5/)</li></ul> | https://github.com/rrwick/Trycycler |
 | [Unicycler](https://hub.docker.com/r/staphb/unicycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/unicycler)](https://hub.docker.com/r/staphb/unicycler) | <ul><li>0.4.7</li><li>0.4.8</li><li>0.4.9</li><li>0.5.0</li></ul> | https://github.com/rrwick/Unicycler |
 | [VADR](https://hub.docker.com/r/staphb/vadr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vadr)](https://hub.docker.com/r/staphb/vadr) | <ul><li>1.1</li><li>1.1.2</li><li>1.1.3</li><li>1.2</li><li>1.2.1</li><li>1.3 & SARS-CoV-2 models 1.3-1</li><li>1.3 & SARS-CoV-2 models 1.3-2</li><li>1.4 & SARS-CoV-2 models 1.3-2</li><li>1.4.1 & SARS-CoV-2 models 1.3-2</li><li>[1.4.2 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1](vadr/1.4.2/)</li><li>[1.5 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1](vadr/1.5/)</li><li>[1.5.1 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2](vadr/1.5.1/)</li><li>[1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1](vadr/1.6.3/)</li><li>[1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1, HAV v1.0.0](vadr/1.6.3-hav/)</li><li>[1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-2, HAV v1.0.0](vadr/1.6.3-hav-flu2/)</li></ul> | https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) </br>https://github.com/ncbi/vadr |
-| [Verkko](https://hub.docker.com/r/staphb/verkko/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/verkko)](https://hub.docker.com/r/staphb/verkko) | <ul><li>[2.0](./verkko/2.0/)</li><li>[2.1](./verkko/2.1/)</li></ul> | https://github.com/marbl/verkko |
+| [Verkko](https://hub.docker.com/r/staphb/verkko/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/verkko)](https://hub.docker.com/r/staphb/verkko) | <ul><li>[2.0](./verkko/2.0/)</li><li>[2.1](./verkko/2.1/)</li><li>[2.2](./verkko/2.2/)</li></ul> | https://github.com/marbl/verkko |
 | [VIBRANT](https://hub.docker.com/r/staphb/vibrant/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vibrant)](https://hub.docker.com/r/staphb/vibrant) | <ul><li>1.2.1</li></ul> | https://github.com/AnantharamanLab/VIBRANT |
 | [VIGOR4](https://hub.docker.com/r/staphb/vigor4/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vigor4)](https://hub.docker.com/r/staphb/vigor4) | <ul><li>[4.1.20190131](./vigor4/4.1.20190131/)</li><li>[4.1.20200702](./vigor4/4.1.20200702/)</li></ul> | https://github.com/JCVenterInstitute/VIGOR4 |
 | [Viridian](https://hub.docker.com/r/staphb/viridian/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/viridian)](https://hub.docker.com/r/staphb/viridian) | <ul><li>[1.2.2](./viridian/1.2.2/)</li></ul> | https://github.com/iqbal-lab-org/viridian |

verkko/2.2/Dockerfile

@@ -0,0 +1,48 @@
+FROM mambaorg/micromamba:1.5.9 AS app
+
+ARG VERKKO_VER="2.2"
+
+USER root
+
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.9"
+LABEL dockerfile.version="1"
+LABEL software="Verkko"
+LABEL software.version="${VERKKO_VER}"
+LABEL description="Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads."
+LABEL website="https://github.com/marbl/verkko"
+LABEL license="https://github.com/marbl/verkko/blob/master/README.licenses"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    procps &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda verkko=${VERKKO_VER} && \
+    micromamba clean -afy
+
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+CMD [ "verkko", "--help" ]
+
+WORKDIR /data
+
+## Test ##
+FROM app AS test
+
+RUN verkko --help
+
+RUN apt-get update && apt-get install --no-install-recommends -y curl
+
+# test data
+RUN curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz &&\
+    curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz -o ont.fastq.gz
+
+# verkko test run
+RUN verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz &&\
+    head asm/assembly.hifi-coverage.csv &&\
+    head -c 1000 asm/assembly.fasta
+

verkko/2.2/README.md

@@ -0,0 +1,21 @@
+# Verkko container
+
+Main tool: [verkko](https://github.com/marbl/verkko)
+
+Code repository: https://github.com/marbl/verkko
+
+Basic information on how to use this tool:
+- executable: verkko
+- help: --help
+- version: --version
+- description: Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads.
+
+Full documentation: https://github.com/marbl/verkko
+
+## Example Usage
+
+```bash
+verkko -d <work-directory> --hifi <hifi-read-files> [--nano <ont-read-files>]
+```
+
+