adding artic version 1.5.8

README.md

@@ -114,7 +114,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [ANIclustermap](https://hub.docker.com/r/staphb/aniclustermap/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/aniclustermap)](https://hub.docker.com/r/staphb/aniclustermap) | <ul><li>[1.3.0](aniclusteramp/1.3.0/)</li><li>[1.4.0](aniclusteramp/1.4.0/)</li></ul> | https://github.com/moshi4/ANIclustermap |
 | [any2fasta](https://hub.docker.com/r/staphb/any2fasta/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/any2fasta)](https://hub.docker.com/r/staphb/any2fasta) | <ul><li>0.4.2</li></ul> | https://github.com/tseemann/any2fasta |
 | [ARIBA](https://hub.docker.com/r/staphb/ariba/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ariba)](https://hub.docker.com/r/staphb/ariba) | <ul><li>[2.14.4](./ariba/2.14.4/)</li><li>[2.14.6](./ariba/2.14.6/)</li><li>[2.14.7](./ariba/2.14.7/)</li></ul> | https://github.com/sanger-pathogens/ariba |
-| [artic](https://hub.docker.com/r/staphb/artic) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic)](https://hub.docker.com/r/staphb/artic) | <ul><li>[1.2.4-1.11.1 (artic-medaka)](artic/1.2.4-1.11.1/)</li><li>[1.2.4-1.12.0 (artic-medaka)](artic/1.2.4-1.12.0/)</li></ul> | https://github.com/artic-network/fieldbioinformatics |
+| [artic](https://hub.docker.com/r/staphb/artic) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic)](https://hub.docker.com/r/staphb/artic) | <ul><li>[1.2.4-1.11.1 (artic-medaka)](artic/1.2.4-1.11.1/)</li><li>[1.2.4-1.12.0 (artic-medaka)](artic/1.2.4-1.12.0/)</li><li>[1.5.8](./artic/1.5.8/)</li></ul> | https://github.com/artic-network/fieldbioinformatics |
 | [artic-ncov2019](https://hub.docker.com/r/staphb/artic-ncov2019) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019)](https://hub.docker.com/r/staphb/artic-ncov2019) | <ul><li>1.3.0</ul> | https://github.com/artic-network/fieldbioinformatics |
 | [artic-ncov2019-epi2me](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-epi2me)](https://hub.docker.com/r/staphb/artic-ncov2019-epi2me) | <ul><li>0.3.10</ul> | https://github.com/epi2me-labs/wf-artic |
 | [artic-ncov2019-medaka](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-medaka)](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) | <ul><li>1.1.0</ul> | https://github.com/artic-network/artic-ncov2019 |

artic/1.5.8/Dockerfile

@@ -0,0 +1,96 @@
+ARG ARTIC_VER=1.5.8
+
+FROM mambaorg/micromamba:1.5.8 AS app
+
+ARG ARTIC_VER
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="artic"
+LABEL software.version="${ARTIC_VER}"
+LABEL description="A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore"
+LABEL website="https://github.com/artic-network/fieldbioinformatics"
+LABEL license="https://github.com/artic-network/fieldbioinformatics/blob/master/LICENSE"
+LABEL sop="https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+USER root
+WORKDIR /
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps \
+    gcc \
+    make \
+    pkg-config \
+    zlib1g-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    libssl-dev \
+    python3-dev \
+    python3-pip \
+    python-is-python3 && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba create -n artic -y -c conda-forge -c bioconda -c defaults \
+    artic=${ARTIC_VER} && \
+    micromamba clean -a -f -y && \
+    mkdir /data
+
+ENV PATH="${PATH}:/opt/conda/envs/artic/bin/" \
+    CONDA_PREFIX="/opt/conda/envs/artic/" \
+    LC_ALL=C.UTF-8
+
+RUN artic_get_models
+
+CMD artic --help
+
+WORKDIR /data
+
+##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
+##### Step 2. Set up the testing stage.                                 #####
+##### The docker image is built to the 'test' stage before merging, but #####
+##### the test stage (or any stage after 'app') will be lost.           #####
+##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
+
+# A second FROM insruction creates a new stage
+# new base for testing
+FROM app AS test
+ARG ARTIC_VER
+
+# print help and version info; check dependencies (not all software has these options available)
+# Mostly this ensures the tool of choice is in path and is executable
+RUN artic --help && \
+    artic --version
+
+WORKDIR /
+
+# test that came with artic
+RUN wget -q https://github.com/artic-network/fieldbioinformatics/archive/refs/tags/v${ARTIC_VER}.tar.gz && \
+    tar -vxf v${ARTIC_VER}.tar.gz && \
+    cd /fieldbioinformatics-${ARTIC_VER} && ls && \
+    bash ./test-runner.sh clair3
+
+WORKDIR /test
+
+# using on "real" data (sample files were not sequenced with version 5.3.2 primers)
+# filtering fastq files
+RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/050/SRR22452250/SRR22452250_1.fastq.gz && \
+    artic guppyplex --min-length 400 --max-length 700  --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq.gz
+
+# running artic minion with user-provided bed and reference
+RUN wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed && \
+    wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta   && \
+    artic minion --normalise 200 --threads 4  --model ont --read-file SRR22452250_1_filtered.fastq.gz --bed SARS-CoV-2.primer.bed --ref SARS-CoV-2.reference.fasta test1 && \
+    ls test1*
+
+# running artic as it pulls schemes from github
+RUN artic minion --normalise 200 --threads 4  --model ont --read-file SRR22452250_1_filtered.fastq.gz --scheme-name sars-cov-2  --scheme-version  V5.3.2 test2 && \
+    ls test2*
+
+
+RUN echo "included models" && \
+    ls ${CONDA_PREFIX}/bin/models

artic/1.5.8/README.md

@@ -0,0 +1,76 @@
+# artic fieldbioinformatics container
+
+Main tool : [artic](https://github.com/artic-network/fieldbioinformatics)
+
+Full documentation: [https://github.com/artic-network/fieldbioinformatics](https://github.com/artic-network/fieldbioinformatics)
+
+There is also a very useful SOP: [https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html)
+And additional documentation: [https://artic.readthedocs.io/en/latest/](https://artic.readthedocs.io/en/latest/)
+
+> A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.
+
+WARNING : This container does not contain the primer schemes found at [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes). Those will have to be downloaded and mounted separately. There are now commands to download the use the primers at runtime.
+
+This image DOES contain the medaka models downloaded with `artic_get_models`
+
+## Example Usage with the artic primers
+
+```bash
+# filtering reads
+artic guppyplex --min-length 400 --max-length 700  --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq.gz
+
+# downloading medaka models for clair3
+artic_get_models
+
+# running the artic minion workflow
+# the result files will all start with test*
+artic minion --normalise 200 --medaka-model ont --threads 4 --read-file sample.fastq.gz --scheme-directory primer-schemes --scheme-version 5.3.2 nCoV-2019 test
+
+# running the artic minion workflow with user-provided primer bedfiles and references
+artic minion --normalise 200 --threads 4  --model ont --read-file sample.fastq.gz --scheme-name sars-cov-2  --scheme-version  V5.3.2 name
+
+```
+
+In general, any primer scheme can be used as long as it meets [artic's requirements](https://github.com/artic-network/primer-schemes).
+
+
+
+## Medaka models
+
+Artic uses [Clair3](https://github.com/HKU-BAL/Clair3), which uses medaka models. Medaka updates frequently, and artic can throw errors when corresponding ONT models are not found.
+
+These are the medaka models in this image:
+```
+# included models at /opt/conda/envs/artic/bin/models
+hifi
+hifi_revio
+hifi_sequel2
+ilmn
+ont
+ont_guppy5
+r1041_e82_260bps_fast_g632
+r1041_e82_260bps_hac_g632
+r1041_e82_260bps_hac_v400
+r1041_e82_260bps_hac_v410
+r1041_e82_260bps_sup_g632
+r1041_e82_260bps_sup_v400
+r1041_e82_260bps_sup_v410
+r1041_e82_400bps_fast_g632
+r1041_e82_400bps_hac_g615
+r1041_e82_400bps_hac_g632
+r1041_e82_400bps_hac_v400
+r1041_e82_400bps_hac_v410
+r1041_e82_400bps_hac_v420
+r1041_e82_400bps_hac_v430
+r1041_e82_400bps_hac_v500
+r1041_e82_400bps_sup_g615
+r1041_e82_400bps_sup_v400
+r1041_e82_400bps_sup_v410
+r1041_e82_400bps_sup_v420
+r1041_e82_400bps_sup_v430
+r1041_e82_400bps_sup_v500
+r104_e81_hac_g5015
+r104_e81_sup_g5015
+r941_prom_hac_g360+g422
+r941_prom_sup_g5014
+```