Added latest version of dragonflye and updated main README (#683)

* Added version of dragonflye and updated README

* removed git, adjusted labels, added CMD

---------

Co-authored-by: Curtis Kapsak <[email protected]>
Co-authored-by: Young <[email protected]>

README.md

@@ -58,7 +58,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [cutshaw-report-env](https://hub.docker.com/r/staphb/cutshaw-report-env) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cutshaw-report-env)](https://hub.docker.com/r/staphb/cutshaw-report-env) | <ul><li>1.0.0</li></ul> | https://github.com/VADGS/CutShaw |
 | [datasets-sars-cov-2](https://github.com/CDCgov/datasets-sars-cov-2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | <ul><li>0.6.2</li><li>0.6.3</li><li>0.7.2</li></ul> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [dnaapler](https://hub.docker.com/r/staphb/dnaapler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) | <ul><li>[0.1.0](dnaapler/0.1.0/)</li></ul> | https://github.com/gbouras13/dnaapler |
-| [dragonflye](https://hub.docker.com/r/staphb/dragonflye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | <ul><li>1.0.14</li></ul> | https://github.com/rpetit3/dragonflye |
+| [dragonflye](https://hub.docker.com/r/staphb/dragonflye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | <ul><li>1.0.14</li><li>[1.1.1](dragonflye/1.1.1/)</li></ul> | https://github.com/rpetit3/dragonflye |
 | [DSK](https://hub.docker.com/r/staphb/dsk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | <ul><li>0.0.100</li></ul> | https://gatb.inria.fr/software/dsk/ |
 | [emboss](https://hub.docker.com/r/staphb/emboss) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emboss)](https://hub.docker.com/r/staphb/emboss) | <ul><li>6.6.0 (no version)</li></ul> | http://emboss.sourceforge.net |
 | [emmtyper](https://hub.docker.com/r/staphb/emmtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | <ul><li>0.2.0</li></ul> | https://github.com/MDU-PHL/emmtyper |

dragonflye/1.1.1/Dockerfile

@@ -0,0 +1,97 @@
+FROM mambaorg/micromamba:1.4.4 as app
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building; set to /data at the end of app layer
+WORKDIR /
+
+# ARG variables only persist during build time 
+ARG DRAGONFLYE_VER="1.1.1"    
+
+# metadata labels
+LABEL base.image="mambaorg/micromamba:1.4.4"
+LABEL dockerfile.version="1"
+LABEL software="dragonflye"
+LABEL software.version=${DRAGONFLYE_VER}
+LABEL description="Conda environment for dragonflye. Dragonflye: Assemble bacterial isolate genomes from Nanopore reads."
+LABEL website="https://github.com/rpetit3/dragonflye"
+LABEL license="GNU General Public License v3.0"
+LABEL license.url="https://github.com/rpetit3/dragonflye/blob/main/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer1="Erin Young"
+LABEL maintainer1.email="[email protected]"
+
+# install dependencies; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ wget \
+ ca-certificates \
+ procps \
+ bsdmainutils && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# create the conda environment; install dragonflye and dependencies based on bioconda package; cleanup conda garbage
+RUN micromamba install -n base -c conda-forge -c bioconda -c defaults -y dragonflye=${DRAGONFLYE_VER} && \
+ micromamba clean -a -y && \
+ mkdir /data
+
+WORKDIR /data
+
+# hardcode base conda environment into the PATH variable; LC_ALL for singularity compatibility
+ENV PATH="$PATH:/opt/conda/bin/" \
+ LC_ALL=C.UTF-8
+
+CMD dragonflye --help
+
+# new base for testing
+FROM app as test
+
+# so that mamba/conda env is active when running below commands
+ENV ENV_NAME="base"
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# show help options and check dependencies
+RUN dragonflye --help && \
+ dragonflye --check
+
+# so that testing outputs are inside /test
+WORKDIR /test
+
+# download test data (ONT and ILMN FASTQs)
+RUN echo "downloading ILMN and ONT test data from bactopia/bactopia-tests on GitHub..." && \
+    wget https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/nanopore/ERR3772599.fastq.gz && \
+    wget https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/illumina/SRR2838702_R1.fastq.gz && \
+    wget https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/illumina/SRR2838702_R2.fastq.gz
+
+# test assembly and polishing algorithms with test data
+# modified code from here: https://github.com/rpetit3/dragonflye/blob/main/.github/workflows/test-dragonflye.yml
+RUN echo "Testing Raven Assembler (quality filtered)..." && \
+dragonflye --reads /test/ERR3772599.fastq.gz --prefix ERR3772599 --cpus 0 --nopolish --outdir raven-minquality --gsize 300000 --assembler raven --minquality 8 && \
+echo "Test Raven Assembler (quality filtered, no length filter)..." && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir raven-minquality-nominreadlen --gsize 300000 --assembler raven --minquality 6 --minreadlen 0 && \
+echo "Test Raven Assembler (quality filtered, no length filter, trimming)" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir raven-minquality-nominreadlen-trim --gsize 300000 --assembler raven --minquality 6 --minreadlen 0 --trim && \
+echo "Test Raven Assembler (quality filtered, no length filter, trim opts)" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir raven-minquality-nominreadlen-trimopts --gsize 300000 --assembler raven --minquality 6 --minreadlen 0 --trim --trimopts '--adapter_threshold 95' && \
+echo "Testing Raven Assembler" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --prefix ERR3772599-raven --cpus 0 --nopolish --depth 5 --outdir raven --gsize 300000 --assembler raven && \
+echo "Testing Raven Assembler + Racon Polish" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --outdir raven-racon --gsize 300000 --assembler raven && \
+echo "Testing Flye Assembler + Medaka Polish" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --outdir raven-medaka --gsize 300000 --assembler raven --racon 0 --model r103_min_high_g345 && \
+echo "Testing Flye Assembler + Medaka Polish + --medaka_opts" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --outdir raven-medaka-opts --gsize 300000 --assembler raven --racon 0 --model r103_min_high_g345 --medaka_opts '-b 200' && \
+echo "Testing Flye Assembler + Racon & Medaka Polish" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --outdir raven-both --gsize 300000 --assembler raven && \
+echo "Testing Flye Assembler + Racon & Pilon Polish" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --R1 /test/SRR2838702_R1.fastq.gz --R2 /test/SRR2838702_R2.fastq.gz --cpus 0 --outdir raven-polypolish --gsize 300000 --assembler raven && \
+echo "Testing Flye Assembler + Racon & Polypolish Polish" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --R1 /test/SRR2838702_R1.fastq.gz --R2 /test/SRR2838702_R2.fastq.gz --cpus 0 --outdir raven-pilon --gsize 300000 --assembler raven --polypolish 0 --pilon 1 && \
+echo "Testing Miniasm Assembler" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --prefix ERR3772599_mini.asm --cpus 1 --nopolish --outdir miniasm --gsize 300000 --assembler miniasm && \
+echo "Testing Flye Assembler" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir flye --gsize 300000 --assembler flye && \
+echo "Testing Flye Assembler (with --nano-hq)" && \
+dragonflye --reads /test/ERR3772599.fastq.gz --prefix ERR3772599-nano.hq --cpus 0 --nopolish --outdir flyehq --gsize 300000 --assembler flye --nanohq && \
+echo "Testing --list_models" && \
+dragonflye --list_models 2>&1 | grep r941_min_sup_g507

dragonflye/1.1.1/README.md

@@ -0,0 +1,43 @@
+# dragonflye docker image
+
+Main tool : [dragonflye v1.1.1](https://github.com/rpetit3/dragonflye)
+
+> dragonflye: Assemble bacterial isolate genomes from Nanopore reads
+
+## Additional tools
+
+Protip: run command `docker run staphb/dragonflye:latest micromamba list` to see full micromamba environment:
+
+- [any2fasta 0.4.2](https://github.com/tseemann/any2fasta)
+- [assembly-scan 0.4.1](https://github.com/rpetit3/assembly-scan)
+- [bwa 0.7.17-r1188](https://github.com/lh3/bwa)
+- [bcftools 1.15.1](https://github.com/samtools/bcftools)
+- biopython 1.80
+- [fastp 0.23.2](https://github.com/OpenGene/fastp)
+- [flye 2.9.1](https://github.com/fenderglass/Flye)
+- [kmc 3.2.1](https://github.com/refresh-bio/KMC)
+- [medaka 1.6.1](https://github.com/nanoporetech/medaka)
+- [miniasm 0.3](https://github.com/lh3/miniasm)
+- [minimap2 2.24-r1122](https://github.com/lh3/minimap2)
+- [nanoq 0.9.0](https://github.com/esteinig/nanoq)
+- perl 5.32.1
+- [pigz 2.6](https://zlib.net/pigz/)
+- [polypolish 0.5.0](https://github.com/rrwick/Polypolish)
+- [porechop 0.2.4](https://github.com/rrwick/Porechop)
+- python 3.8.15
+- [racon 1.5.0](https://github.com/lbcb-sci/racon)
+- [rasusa 0.7.0](https://github.com/mbhall88/rasusa)
+- [raven 1.8.1](https://github.com/lbcb-sci/raven)
+- [samclip 0.4.0](https://github.com/tseemann/samclip)
+- [samtools 1.15.1](https://github.com/samtools/samtools)
+- [seqtk 1.3-r106](https://github.com/lh3/seqtk)
+
+## Example Usage
+
+```bash
+# download ONT FASTQs for testing
+wget https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/nanopore/ERR3772599.fastq.gz
+
+# run dragonflye using flye as the assembly algorithm
+dragonflye --reads /test/ERR3772599.fastq.gz --prefix ERR3772599-nano.hq --cpus 0 --nopolish --outdir flyehq --gsize 300000 --assembler flye --nanohq
+```